Introduction to Bioinformatics

Molecular Biology Primer

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 Genetic Material
• DNA (deoxyribonucleic acid) is the genetic
material
• Information stored in DNA
– the basis of inheritance
– distinguishes living things from nonliving
things
• Genes
– various units that govern living thing’s
characteristics at the genetic level

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 Nucleotides
• Genes themselves contain their information as a specific
sequence of nucleotides found in DNA molecules
• Only four different bases in DNA molecules
– Guanine (G)
– Adenine (A) Base
– Thymine (T)
P
– Cytosine (C) Sugar

• Each base is attached to a phosphate group and a

deoxyribose sugar to form a nucleotide.
• The only thing that makes one nucleotide different from
another is which nitrogenous base it contains

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Purine:

Pyrimidine:

Nucleoside

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 Nucleotides
• Complicated genes can be many
thousands of nucleotides long
• All of an organism’s genetic instructions,
its genome, can be maintained in millions
or even billions of nucleotides

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 Orientation
• Strings of nucleotides can be attached to
each other to make long polynucleotide
chains
• 5’ (5 prime) end
– The end of a string of nucleotides with a 5'
carbon not attached to another nucleotide
• 3’ (3 prime) end
– The other end of the molecule with an
unattached 3' carbon

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5’ 1’
4’ 2’
3’

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 Base Pairing
• Structure of DNA
– Double helix
– Seminal paper by Watson and Crick in 1953
– Rosalind Franklin’s contribution
• Information content on one of those strands
essentially redundant with the information on the
other
– Not exactly the same—it is complementary
• Base pair
– G paired with C (G  C)
– A paired with T (A = T)
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 Base Pairing
• Reverse complements
– 5' end of one strand corresponding to the 3' end of its
complementary strand and vice versa
• Example
– one strand: 5'-GTATCC-3'
the other strand: 3'-CATAGG-5'  5'-GGATAC-3'
• Upstream: Sequence features that are 5' to a
particular reference point
• Downstream: Sequence features that are 3' to a
particular reference point
5' 3'
Upstream Downstream
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DNA Structure

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DNA Structure

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 Chromosome
• Threadlike "packages" of genes and other
DNA in the nucleus of a cell

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 Chromosome
• Different kinds of organisms have different
numbers of chromosomes
• Humans
– 23 pairs
– 46 in all

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 Central Dogma of Molecular
Biology
• DNA: information storage
• Protein: function unit, such as enzyme
• Gene: instructions needed to make protein
• Central dogma

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 Central Dogma of Molecular
Biology
• Central dogma

reverse transcription
(reverse transcriptase)
replication
(DNA polymerase)
• DNA obtained from reverse transcription is
called complementary DNA (cDNA)
 Difference between DNA and cDNA will be
discussed later 17
 Central Dogma of Molecular
Biology
• RNA (ribonucleic acid) DNA
Base
– Single-stranded polynucleotide
P
– Bases Sugar
• A
H
• G
RNA
• C Base
• U (uracil), instead of T P
Sugar
• Transcription (simplified …)
– A  A, G G, C  C, T  U OH

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DNA Replication (DNA  DNA)

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DNA Replication (DNA  DNA)

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 DNA Replication Animation

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Courtesy of Rob Rutherford, St. Olaf University
 Transcription (DNA  RNA)
• Messenger RNA (mRNA)
– carries information to be
translated
• Ribosomal RNA (rRNA)
– the working “spine” of
the ribosome
• Transfer RNA (tRNA)
– the “decoder keys” that
will translate nucleic
acids to amino acids

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 Transcription Animation

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Courtesy of Rob Rutherford, St. Olaf University
 Peptides and Proteins
• mRNA  Sequence of amino
acids connected by peptide
bond
• Amino acid sequence
– Peptide: < 30 – 50 amino acids
– Protein: longer peptide

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 Genetic Code – Codon

Codon:
3-base
RNA Stop
codons
sequence

Start
codon
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 List of Amino Acids
Amino acid Symbol Codon
A Alanine Ala GC*
C Cysteine Cys UGU, UGC
D Aspartic Acid Asp GAU, GAC
E Glutamic Acid Glu GAA, GAG
F Phenylalanine Phe UUU, UUC
G Glycine Gly GG*
H Histidine His CAU, CAC
I Isoleucine Ile AUU, AUC, AUA
K Lysine Lys AAA, AAG
L Leucine Leu UUA, UUG, CU*
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 List of Amino Acids
Amino acid Symbol Codon
M Methionine Met AUG
N Asparagine Asn AAU, AAC
P Proline Pro CC*
Q Glutamine Gln CAA, CAG
R Arginine Arg CG*, AGA, AGG
S Serine Ser UC*, AGU, AGC
T Threonine Thr AC*
V Valine Val GU*
W Tryptophan Trp UGG
Y Tyrosine Tyr UAU, UAC

20 letters, no B J O U X Z 31
 Codon and Reading Frame
• 4 AA letters  43 = 64 triplet possibilities
• 20 (< 64) known amino acids
• Wobbling 3rd base
• Redundant  Resistant to mutation
• Reading frame: linear sequence of codons in a
gene
• Open Reading Frame (ORF), definition varies:
– a reading frame that begins with a start codon and
end at a stop codon
– a series of codons in a DNA sequence uninterrupted
by the presence of a stop codon
 a potential protein-coding region of DNA sequence
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 Open Reading Frame
• Given a nucleotide sequence
– How many reading frames? __
• __ forward and __ backward
• Example: Given a DNA sequence,
5’-ATGACCGTGGGCTCTTAA-3’
– ATG ACC GTG GGC TCT TAA  M T V G S *
– TGA CCG TGG GCT CTT AA  * P W A L
– GAC CGT GGG CTC TTA A  D R G L L
– Figure out the three backward reading frames
• In random sequence, a stop codon will follow a Met in
~20 AAs
• Substantially longer ORFs are often genes or parts of
them
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Translation (RNA  Protein)

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 Translation Animation

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Courtesy of Rob Rutherford, St. Olaf University
 Gene Expression
• Gene expression
– Process of using the information stored in
DNA to make an RNA molecule and then a
corresponding protein
• Cells controlling gene expression by
– reliably distinguishing between those parts of
an organism’s genome that correspond to the
beginnings of genes and those that do not
– determining which genes code for proteins
that are needed at any particular time.
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 Promoter
• The probability (P) that a string of nucleotides will occur
by chance alone if all nucleotides are present at the same
frequency P = (1/4)n, where n is the string’s length
• Promoter sequences
– Sequences recognized by RNA polymerases as being associated
with a gene
• Example
– Prokaryotic RNA polymerases scan along DNA looking for a
specific set of approximately 13 nucleotides marking the
beginning of genes
– 1 nucleotide that serves as a transcriptional start site
– 6 that are 10 nucleotides 5' to the start site, and
– 6 more that are 35 nucleotides 5' to the start site
– What is the frequency for the sequence to occur?
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 Gene Regulation
• Regulatory proteins
– Capable of binding to a cell’s DNA near the promoter
of the genes
– Control gene expression in some circumstances but
not in others
• Positive regulation
– binding of regulatory proteins makes it easier for an
RNA polymerase to initiate transcription
• Negative regulation
– binding of the regulatory proteins prevents
transcription from occurring

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Promoter and Regulatory Example

• Low tryptophan concentration

 RNA polymerase binds to promoter
 genes transcribed
• High tryptophan concentration
 repressor protein becomes active and binds to operator
 blocks the binding of RNA polymerase to the promoter
• Tryptophan concentration drops
 repressor releases its tryptophan and is released from DNA
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 polymerase again transcribes genes
Gene Structure

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Exons and Introns

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Exons and Introns Example

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 Protein Structure and Function
• Genes encode the recipes for proteins

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 Protein Structure and Function
• Proteins are amino acid polymers

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 Proteins: Molecular Machines
 Proteins in your muscles allows you to move:
myosin
and
actin

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 Proteins: Molecular Machines
 Digestion, catalysis
(enzymes)
 Structure (collagen)

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 Proteins: Molecular Machines
 Signaling
(hormones,
kinases)
 Transport
(energy,
oxygen)

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Protein
Structures

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Information Flow in Nucleated Cell

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 Point Mutation Example:
Sickle-cell Disease
• Wild-type hemoglobin • Mutant hemoglobin
DNA DNA
3’----CTT----5’ 3’----CAT----5’

mRNA mRNA
5’----GAA----3’ 5’----GUA----3’

Normal hemoglobin Mutant hemoglobin

------[Glu]------ ------[Val]------
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image credit: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis.
 Thinking about the Human
Genome
50% is high copy number repeats
About 10% is transcribed
(made into RNA)
Only 1.5% actually codes for protein
98.5% Junk DNA

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Thinking about the Human
Genome
~ 3 X 109 bps
(3 billion base pairs)

If each base were one mm long…

2000 miles, across the center of Africa
Average gene about 30 meters long
Occur about every 270 meters between them
Once spliced the message would only be
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~1 meter long