Introduction to Bioinformatics

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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 things
  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)
• Thymine (T)
• Cytosine (C)
• 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

Base
P
Sugar
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Purine
Pyrimidine
Nucleoside
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Nucleotides

• Complicated genes can be many thousands of
  nucleotides long
• All of an organisms 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
2
4
3
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Base Pairing

• Structure of DNA
• Double helix
• Seminal paper by Watson and Crick in 1953
• Rosalind Franklins contribution
• Information content on one of those strands
  essentially redundant with the information on the
  other
• Not exactly the sameit 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

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Central Dogma of Molecular Biology

• RNA (ribonucleic acid)
• Single-stranded polynucleotide
• Bases
• A
• G
• C
• U (uracil), instead of T
• Transcription (simplified )
• A ? A, G ?G, C ? C, T ? U

DNA
H
RNA
OH
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DNA Replication (DNA ? DNA)
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DNA Replication (DNA ? DNA)
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DNA Replication Animation
Courtesy of Rob Rutherford, St. Olaf University
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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
Courtesy of Rob Rutherford, St. Olaf University
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Peptides and Proteins

• mRNA ? Sequence of amino acids connected by
  peptide bond
• Amino acid sequence
• Peptide lt 30 50 amino acids
• Protein longer peptide

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Genetic Code Codon

• Codon
• 3-base RNA sequence

Stop codons
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

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Codon and Reading Frame

• 4 AA letters ? 43 64 triplet possibilities
• 20 (lt 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
Courtesy of Rob Rutherford, St. Olaf University
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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
  organisms 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 strings 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 cells 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
• ? polymerase again transcribes genes

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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
  movemyosinandactin

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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
• DNA
• 3----CTT----5
• mRNA
• 5----GAA----3
• Normal hemoglobin
• ------Glu------

• Mutant hemoglobin
• DNA
• 3----CAT----5
• mRNA
• 5----GUA----3
• Mutant hemoglobin
• ------Val------

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image credit U.S. Department of Energy Human
Genome Program, http//www.ornl.gov/hgmis.
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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
• 1 meter long