Introduction to Molecular Biology and Genomics

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Introduction to Molecular Biology and Genomics

• Part One of a Short Course Series
• Functional Genomics and Computational Biology
• Greg Gonye
• Research Assistant Professor of Pathology Anatomy
  and Cell Biology
• Daniel Baugh Institute for Functional Genomics
  and Computational Biology

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Context

• Past decade and 100s of millions of tax dollars
  to determine the sequence of the human
  genome. What does this mean, why do we care,
  what can we do with it
• Parallel increase in access to computational
  power
• Opportunity and need to train new breed of
  scientist blending biology and engineering
  strengths to exploit the technologies available
  on a new scale

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Short Course Series

• First steps towards a joint degree program with
  UD School of Engineering
• Refinement of content and pace
• Evaluation of interest/need
• Tele-teaching technology
• - Introduction to Molecular Biology and Genomics
  (Oct-Nov)
• - Computational Biology (Jan-Feb)
• - Bioinformatics (Mar-Apr)

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Intro to Mol. Biol. And Genomics

• High level objective to build foundation required
  to participate in the second and third classes of
  the series as well as outside the classes
• Team taught by faculty involved in application of
  technologies
• Introduction of molecular biology of cells and
  the technology it has spawned

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At Finer Grain

• History of molecular biologys origins
• Introduction of technologies resulting from these
  biological discoveries
• Create glossary of terms and jargon
• Focus on large-scale high throughput technologies
  supporting genome scale science
• Use experimental examples when possible

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• Computational Biology (Jan-Feb)
• Focus will be modeling approaches and utility of
  modeling and simulation of biological systems
• Frank Doyle
• Professor of Chemical Engineering, UDel
  fdoyle_at_udel.edu
• Bioinformatics (Mar-Apr)
• Focus will be use of computation in the analysis
  of different classes of data being generated by
  structural and functional genomics
• James Schwaber
• Professor of Pathology Anatomy and Cell Biology,
  TJU james.schwaber_at_mail.tju.edu

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Session I From peas to helixes

• Outline
• Inherited trait
• Role of chromosomes
• gene equals protein
• genes are DNA
• structure of DNA

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Inheritance something is getting passed along
factors (Mendel, 1865)
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Mendels Experiments
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Mendelian Genetics

• Alleles
• dominant and recessive
• Traits (phenotype) result of passage of factors
  (genotype) from parents to offspring
• Predictable therefore discrete entities

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It was the Columbia-ns

• 1902-1910 researchers at Columbia University make
  great strides
• Sutton coins the word gene and suggests
  chromosomes as the home of genes due to pairs
  in somatic cells and singlets in the gametes
• Wilson confirms by demonstrating that sex is
  determined by specific chromosomes the X and Y
• Morgan starts modern era of genetics with a new
  model system, Drosophila melanogaster, the
  fruitfly

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Do chromosomes carry genes?
Stages of somatic cell division Mitosis
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It was the Columbia-ns

• 1902-1910 researchers at Columbia University make
  great strides
• Sutton coins the word gene and suggests
  chromosomes as the home of genes due to pairs
  in somatic cells and singlets in the gametes
• Wilson confirms by demonstrating that sex is
  determined by specific chromosomes the X and Y
• Morgan starts modern era of genetics with a new
  model system, Drosophila melanogaster, the
  fruitfly

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Morgan, cont

• White eyed mutant fly in population of red eyed
  wild type
• Trait followed Mendels predictions for recessive
  sex-linked allele only males, half the time
  gene mapped to a specific chromosome, X
• Morgan et al., from many more mutants, discovered
  linkage, genes which seemed to travel together,
  and recombination, the physical rearrangement of
  the chromosomes, ultimately developing a measure
  of distance between genes, the morgan

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One GenegtgtOne Protein
Beadle and Tatum (Stanford) 1941 genes equal
enzymes, enzymes equal pathways
Used X-ray mutagenesis to create defective genes
in the bread mold Neurospora. Followed growth
on different types of media to identify many
enzyme genes. Some grew on the same media
therefore identifying genes forming a multistep
pathway to synthesis of a product
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DNA is the principle
Griffith 1928 Virulent/smooth pneumococcus vs.
Avirulent/rough pneumococcus Killed smooth
bacteria contained transforming principle to
convert avirulent rough to live and deadly smooth
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Proof of Principle?

• Avery et al. (Rockefeller) spent the next 15
  years trying to identify the transforming
  principle of Griffith
• Not the coat itself
• Most active fraction contained mostly
  deoxyribonucleic acid (DNA)
• Not sensitive to proteases
• Not sensitive to ribonucleases
• Highly sensitive to deoxyribonuclease
• Unfortunately conventional wisdom was leaning
• towards protein(s) so DNA was labeled scaffold
• for trace protein component

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Proof of Principle!!
Hershey and Chase 1952 combined use of T4
bacteriophage and isotopic labeling to prove DNA
was the transforming agent
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Summary of past 100 years

• Genes are discrete information for different
  traits and proteins
• Collectively genes are a genotype encoding a
  phenotype
• genes are physically encoded in DNA
• DNA is organized into chromosomes
• chromosomes are inherited from parent(s)
• Avery busted his butt and got rooked
• Hershey or Chase may have invented the frozen
  daiquiris

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Discussion Point for the Break

• Darwin and Mendel were contemporaries. Imagine
  what that discussion would have been like if they
  had met...

After the Break The pretty molecule
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Chemistry of DNA

• DNA was originally isolated in 1869 from white
  cells off of bandages
• By the time of the Columbia work a lot was known
• nucleic acids were very long molecules
• three subunits a 5 carbon sugar, a phosphate,
  and 5 types of nitrogenous bases, adenine,
  thymine, cytosine, guanine and uracil
• By Hershey and Chase more
• two types ribonucleic and deoxyribonucleic with
  thymine found only in the deoxy- form and uracil
  only in the ribo- form

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Additional Information

• Finally by 1952
• Linus Paulings description of chemical bond
  properties resulted in the structures of the
  different subunits

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Additional Information cont

• Chargaff (Columbia again) demonstrates a one to
  one ratio of adenine to thymine and guanine to
  cytosine
• Wilkins and Franklin (Cambridge U) generated
  X-ray crystallography data suggesting a repeating
  helical structure

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Watson and Cricks Double helix

• Needed molecule to fit structural constraints
• Needed to keep bases equal
• Needed molecule with ability to replicate
• Needed molecule to store enormous amount of
  information from 4 letter alphabet
• Used paper, wire, and ring stands to figure it out

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Go to Netscape and Chime
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Antiparallel Polarity
5 to 3
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Summary of DNA structure features

• Double stranded helix, sugar-phosphate backbone
• Hydrogen bonding between bases maintains
  structure
• A-T and G-C only, but any order
• colinearity and self replication information
• Polarity of polymer 5 end and 3 end

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Information Storage Genome Structure

• Very Different Procaryotes vs. Eucaryotes
• Bacteria use Operons
• Eucaryotes use Genes
• Exons and Introns
• Control Elements
• Promoters start transcription
• Promoters are controlled by operators/enhancers
• Terminators stop transcription in bacteria,
  Processivity stops transcription in eucaryotes
  but ends are made by a polyadenylation signal

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Operons in Bacteria
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Exons and Introns in Eucaryotes
intron1
exon 1
exon 2
intron 2
DNA
mature RNA
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Ribonucleic acid (RNA)

• Essentially single strand of helix so available
  to self-basepair to generate 3D structures

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• small nuclear RNA (snRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)

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Types of RNA molecules

• ribosomal RNA (rRNA)
• many copies in genome
• structural RNA for assembly of ribosome, part of
  protein synthesis machinary
• large precursor molecule specifically cut into
  smaller parts
• specific RNA polymerase to handle rRNA synthesis
• transfer RNA (tRNA)
• small nuclear RNA (snRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• product of own gene or part of rRNA precursor
• small uniform size, varied amounts of each
• part of protein synthesis process
• transfers information from nucleic acid to
  protein
• small nuclear RNA (snRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• heteronuclear RNA (hnRNA)
• varies in size from 100 bases to 12,000 bases
• unstable intermediates to other types of RNA
  populations
• mostly immature messenger RNA
• messenger RNA (mRNA)
• small nuclear RNA (snRNA)

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)
• encodes instructions for protein assembly
• in eukaryotics is highly processed in nucleus to
  produce mature form in the cytoplasm
• similar size range to hnRNA
• small nuclear RNA (snRNA)

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)
• small nuclear RNA (snRNA)
• stable due to specific interactions with nuclear
  proteins to from snrps (small nuclear
  riboproteins)
• diversity of types define different steps of
  processing
• catalytic species involved in RNA processing

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Types of RNA molecules

• ribosomal RNA (rRNA)
• transfer RNA (tRNA)
• small nuclear RNA (snRNA)
• heteronuclear RNA (hnRNA)
• messenger RNA (mRNA)

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Colinearity of information

• DNA molecule has directionality
• DNA encodes genes
• RNA extracts information from storage
• Genes represent proteins
• Colinearity of information between DNA and
  proteins
• DNA sequence is deterministic of protein
  function (through structure we will find out)

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Biological Information Flow Central Dogma
TACTGACGAAAA ATGACTGCTTTT
DNA
transcription
splicing (higher organisms)
RNA
AUGACUGCUUUU
translation
Protein
Met-Thr-Ala-Phe