Introduction to Bioinformatics

1
Introduction to Bioinformatics

• Molecular Biology Primer

2
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

3
Nucleotides

• Genes themselves contain their information as a
  specific sequence of nucleotides found in DNA
  molecules
• Only four different bases used 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
4
Nucleoside
5
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

6
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

7
5
1
2
4
3
8
Base Pairing

• Structure of DNA
• Double helix
• Paper by Watson and Crick in 1953
• 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)

9
(No Transcript)
10
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

11
DNA Structure
12
DNA Structure

• Lets see what Watson and Crick said about their
  discovery

13
Chromosome

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

14
(No Transcript)
15
Chromosome

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

16
Central Dogma of Molecular Biology

• DNA information storage
• Protein function unit, such as enzyme
• Gene instructions needed to make protein
• Central dogma

17
Central Dogma of Molecular Biology

• RNA (ribonucleic acid)
• Single-stranded polynucleotide
• Bases
• A
• G
• C
• U (uracil), instead of T
• Transcription
• A ? A, G ?G, C ? C, T ? U
• Lets see what Crick said about his proposal

DNA
H
RNA
OH
18
(No Transcript)
19
(No Transcript)
20
DNA Replication (DNA ? DNA)
21
DNA Replication (DNA ? DNA)
22
DNA Replication Animation
Courtesy of Rob Rutherford, St. Olaf University
23
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

24
Transcription Animation
Courtesy of Rob Rutherford, St. Olaf University
25
Peptides and Proteins

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

26
(No Transcript)
27
(No Transcript)
28
Genetic Code Codon

• Codon
• 3-base RNA sequence

Stop codons
Start codon
29
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

30
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 (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) a potential
  protein-coding region of DNA sequence
• 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

32
Open Reading Frame

• Given a nucleotide sequence
• What to begin with? ATG
• How many reading frames? 6
• 3 forward and 3 backward
• Example ATGACCGTGGGCTCTTAA
• 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 AA
• Substantially longer ORFs are often genes or
  parts of them

33
Translation (RNA ? Protein)
34
Translation Animation
Courtesy of Rob Rutherford, St. Olaf University
35
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.

36
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

37
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

38
Promoter and Regulatory Example
39
Gene Structure
40
Exons and Introns
41
Exons and Introns Example
42
General sequence of steps in the formation of
eukaryotic mRNA
Courtesy of Ben King, Jackson Lab
43
Protein Structure and Function

• Genes encode the recipes for proteins

44
Protein Structure and Function

• Proteins are amino acid polymers

45
Proteins Molecular Machines

• Proteins in your muscles allows you to
  movemyosinandactin

46
Proteins Molecular Machines

• Enzymes(digestion, catalysis)
• Structure (collagen)

47
Proteins Molecular Machines

• Signaling(hormones, kinases)
• Transport(energy, oxygen)

48
Protein Structures
49
Information Flow in Nucleated Cell
50
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------

51
image credit U.S. Department of Energy Human
Genome Program, http//www.ornl.gov/hgmis.
52
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

53
Thinking about the Human Genome

• 3.2X109 bp
• 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 1meter
  long