Lecture1 20060306 Kang

Introduction to Bioinformatics
Lecture 1:
Overview
Introduction to Bioinformatics National Genome Information Center Spring 2006 (original author: Dr. Eric Rouchka)
Suggested Texts
Bioinformatics: Sequence and Genome
Analysis. David Mount. 2001. ISBN: 9-
87969-608-7.

Biological Sequence Analysis: Probabilistic
models of proteins and nucleic acids. R.
Durbin, S. Eddy, A. Krogh and G. Mitchison.
1998. ISBN: 0-521-62971-3.

Suggested Texts
•
Image Source: http://www.amazon.com/

Other Bioinformatics Books
Other Reference Books
What is Bioinformatics/
Computational Biology?
• Bioinformatics: collection and storage of biological
information
• Computational biology: development of algorithms

and statistical models to analyze biological data
• Bioinformatics/Computational Biology will be

interchanged
What is Bioinformatics?
Source: http://ccb.wustl.edu/
Why should I care?
• SmartMoney ranks
Bioinformatics as #1 among
next HotJobs
• Business Week 50 Masters

of Innovation
• Jobs available, exciting

research potential
• Important information
waiting to be decoded!
http://smartmoney.com/consumer/index.cfm?story=working-june02
Why is bioinformatics hot?
• Supply/demand: few people adequately
trained in both biology and computer science
• Genome sequencing, microarrays, etc lead to

large amounts of data to be analyzed
• Leads to important discoveries
• Saves time and money
What skills are needed?
• Well-grounded in one of the following
areas:
– Computer science
– Molecular biology
– Statistics
• Working knowledge and appreciation in

the others!
Where Can I Learn More?
• ISCB: http://www.iscb.org/
• NBCI: http://ncbi.nlm.nih.gov/
• http://www.bioinformatics.org/
• Journals
• Conferences (ISMB, RECOMB, PSB…)
Overview of Molecular Biology
• Cells
• Chromosomes
• DNA
• RNA
• Amino Acids
• Proteins
• Genome/Transcriptome/Proteome
Cells
• Complex system enclosed
in a membrane
• Organisms are unicellular

(bacteria, baker’s yeast) or
multicellular
• Humans:
– 60 trillion cells
– 320 cell types
Example Animal Cell

www.ebi.ac.uk/microarray/ biology_intro.htm
Organisms
• Classified into two types:
• Eukaryotes: contain a membrane-bound nucleus and

organelles (plants, animals, fungi,…)
• Prokaryotes: lack a true membrane-bound nucleus

and organelles (single-celled, includes bacteria)
• Not all single celled organisms are

prokaryotes!
Chromosomes
• In eukaryotes, nucleus
contains one or several
double stranded DNA
molecules orgainized as
chromosomes
• Humans:
– 22 Pairs of autosomes
– 1 pair sex chromosomes
Human Karyotype
http://avery.rutgers.edu/WSSP/StudentScholars/
Session8/Session8.html
Image source: www.biotec.or.th/Genome/whatGenome.html
What is DNA?
• DNA: Deoxyribonucleic Acid
• Single stranded molecule (oligomer,

polynucleotide) chain of nucleotides
• 4 different nucleotides:
– Adenosine (A)
– Cytosine (C)
– Guanine (G)
– Thymine (T)
Nucleotide Bases
• Purines (A and G)
• Pyrimidines (C and T)
• Difference is in base structure
Image Source: www.ebi.ac.uk/microarray/ biology_intro.htm
DNA
• Can be thought of as an alphabet with 4
characters
• 4 letter alphabet with sufficiently long words

contains information to create complex
organisms
• Not unlike a computer with a small alphabet
DNA polynucleotides(oligomers)
• Different nucleotides are
strung together to form
polynucleotides
• Ends of the
polynucleotide are
different
• A directionality is
present
• Convention is to label
the coding strand from
5’ to 3’
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDNAMOLGEN.html
Single Strand Polynucleotide
Example polynucleotide:
5’ GTAAAGTCCCGTTAGC 3’
Double Stranded DNA
• DNA can be single-stranded or double-stranded
• Double stranded DNA: second strand is the “reverse

complement” strand
• Reverse complement runs in opposite direction and bases

are complementary
• Complementary bases:
– A, T
– C, G
Double Stranded Sequence
Example double stranded polynucleotide:
5’ GTAAAGTCCCGTTAGC 3’
| | | | | | | | | | | | | | | |
3’ CATTTCAGGGCAATCG 5’
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDNAMOLGEN.html
Double Stranded DNA
Double Helix
• Two complementary DNA strands form a stable DNA
double helix
• This spring marks the 50th anniversary of its discovery
Image source; www.ebi.ac.uk/microarray/ biology_intro.htm
RNA
• Ribonucleic Acid
• Similar to DNA
• Thymine (T) is replaced by uracil (U)
• RNA can be:

– Single stranded
– Double stranded
– Hybridized with DNA
RNA
• RNA is generally single stranded
• Forms secondary or tertiary structures
• RNA folding will be discussed later
• Important in a variety of ways, including

protein synthesis
RNA secondary
structure
• E. coli Rnase P
RNA secondary
structure
Image source: www.mbio.ncsu.edu/JWB/MB409/lecture/ lecture05/lecture05.htm
mRNA
• Messenger RNA
• Linear molecule encoding genetic

information copied from DNA molecules
• Transcription: process in which DNA is

copied into an RNA molecule
mRNA processing
• Eukaryotic genes can be pieced together
– Exons: coding regions
– Introns: non-coding regions
• mRNA processing removes introns, splices

exons together
• Processed mRNA can be translated into a

protein sequence
mRNA Processing
Image source: http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm
tRNA
• Transfer RNA
• Well-defined three-dimensional
structure
• Critical for creation of proteins
tRNA structure
tRNA
• Amino acid attached to each tRNA
• Determined by 3 base anticodon sequence

(complementary to mRNA)
• Translation: process in which the nucleotide

sequence of the processed mRNA is used in
order to join amino acids together into a
protein with the help of ribosomes and tRNA
Genetic Code
• 4 possible bases (A, C, G, U)
• 3 bases in the codon
• 4 * 4 * 4 = 64 possible codon sequences
• Start codon: AUG
• Stop codons: UAA, UAG, UGA
• 61 codons to code for amino acids (AUG as
well)
• 20 amino acids – redundancy in genetic code
20 Amino Acids
• Glycine (G, GLY)
• Alanine (A, ALA)
• Valine (V, VAL)
• Leucine (L, LEU)
• Isoleucine (I, ILE)
• Phenylalanine (F, PHE)
• Proline (P, PRO)
• Serine (S, SER)
• Threonine (T, THR)
• Cysteine (C, CYS)
• Methionine (M, MET)
• Tryptophan (W, TRP)
• Tyrosine (T, TYR)
• Asparagine (N, ASN)
• Glutamine (Q, GLN)
• Aspartic acid (D, ASP)
• Glutamic Acid (E, GLU)
• Lysine (K, LYS)
• Arginine (R, ARG)
• Histidine (H, HIS)
• START: AUG
• STOP: UAA, UAG, UGA
Amino Acids
• building blocks for proteins (20 different)
• vary by side chain groups
• Hydrophilic amino acids are water soluble

• Hydrophobic are not
• Linked via a single chemical bond (peptide bond)
• Peptide: Short linear chain of amino acids (< 30) polypeptide:

long chain of amino acids (which can be upwards of 4000
residues long).
Proteins
• Polypeptides having a three dimensional structure.

• Primary–sequence of amino acids constituting the polypeptide
chain
• Secondary–local organization into secondary structures
such as  helices and  sheets
• Tertiary –three dimensional arrangements of the amino acids
as they react to one another due to the polarity and resulting
interactions between their side chains
• Quaternary–number and relative positions of the protein
subunits
Protein Structure
Central Dogma
DNA

RNA

PROTEIN
Central Dogma
What is a Gene?
• the physical and functional unit of
heredity that carries information from
one generation to the next
• DNA sequence necessary for the

synthesis of a functional protein or RNA
molecule
Genome
• chromosomal DNA of an organism
• number of chromosomes and genome size

varies quite significantly from one organism to
another
• Genome size and number of genes does not

necessarily determine organism complexity
Genome Comparison
ORGANISM CHROMOSOMES GENOME SIZE GENES
Homo sapiens 23 3,200,000,000 ~ 30,000

(Humans)
Mus musculus 20 2,600,000,000 ~30,000

(Mouse)
Drosophila 4 180,000,000 ~18,000

melanogaster
(Fruit Fly)
Saccharomyces 16 14,000,000 ~6,000

cerevisiae (Yeast)
Zea mays (Corn) 10 2,400,000,000 ???
Transcriptome
• complete collection of all possible mRNAs
(including splice variants) of an organism.
• regions of an organism’s genome that get

transcribed into messenger RNA.
• transcriptome can be extended to include all

transcribed elements, including non-coding
RNAs used for structural and regulatory
purposes.
Proteome
• the complete collection of proteins that
can be produced by an organism.
• can be studied either as static (sum of

all proteins possible) or dynamic (all
proteins found at a specific time point)
entity

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Introduction to Bioinformatics

Image Source: http://www.amazon.com/

Image Source: http://www.amazon.com/

Image Source: http://www.amazon.com/

• Computational biology: development of algorithms

• Bioinformatics/Computational Biology will be

• Business Week 50 Masters

• Jobs available, exciting

• Genome sequencing, microarrays, etc lead to

• Leads to important discoveries

• Saves time and money

• Working knowledge and appreciation in

• Organisms are unicellular

Example Animal Cell

• Eukaryotes: contain a membrane-bound nucleus and

• Prokaryotes: lack a true membrane-bound nucleus

• Not all single celled organisms are

• Single stranded molecule (oligomer,

Image Source: www.ebi.ac.uk/microarray/ biology_intro.htm

• 4 letter alphabet with sufficiently long words

• Not unlike a computer with a small alphabet

• Double stranded DNA: second strand is the “reverse

• Reverse complement runs in opposite direction and bases

• This spring marks the 50th anniversary of its discovery

Image source; www.ebi.ac.uk/microarray/ biology_intro.htm

• Thymine (T) is replaced by uracil (U)

• RNA can be:

• Forms secondary or tertiary structures

• RNA folding will be discussed later

• Important in a variety of ways, including

Image source: www.mbio.ncsu.edu/JWB/MB409/lecture/ lecture05/lecture05.htm

• Linear molecule encoding genetic

• Transcription: process in which DNA is

• mRNA processing removes introns, splices

• Processed mRNA can be translated into a

Image source: http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm

• Critical for creation of proteins

• Determined by 3 base anticodon sequence

• Translation: process in which the nucleotide

• Hydrophilic amino acids are water soluble

• Linked via a single chemical bond (peptide bond)

• Peptide: Short linear chain of amino acids (< 30) polypeptide:

• DNA sequence necessary for the

• number of chromosomes and genome size

• Genome size and number of genes does not

ORGANISM CHROMOSOMES GENOME SIZE GENES

Homo sapiens 23 3,200,000,000 ~ 30,000

Mus musculus 20 2,600,000,000 ~30,000

Drosophila 4 180,000,000 ~18,000

Saccharomyces 16 14,000,000 ~6,000

Zea mays (Corn) 10 2,400,000,000 ???

• regions of an organism’s genome that get

• transcriptome can be extended to include all

• can be studied either as static (sum of

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