Introduction to Molecular Biology and Genomics

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
Context
Past decade and 100’s 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
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)
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
At Finer Grain
History of molecular biology’s 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 [email protected]
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 [email protected]
Session I: From peas to helixes
Outline:
Inherited “trait”
Role of chromosomes
gene equals protein
genes are DNA
structure of DNA
Inheritance: something is getting passed along: “factors” (Mendel, 1865)
Mendel’s Experiments
Mendelian Genetics
Alleles
dominant and recessive
Traits (phenotype) result of passage of “factors” (genotype) from parents to offspring
Predictable therefore discrete entities
“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

Do chromosomes carry genes?
Stages of somatic cell division: Mitosis
“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

Morgan, con’t
White eyed “mutant” fly in population of red eyed wild type
Trait followed Mendel’s 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


One Gene>>One 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
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
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
Proof of “Principle”!!
Hershey and Chase 1952: combined use of T4 bacteriophage
and isotopic labeling to prove DNA was the transforming agent
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
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”
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
Additional Information
Finally by 1952:
Linus Pauling’s description of chemical bond properties resulted in the structures of the different subunits
Additional Information con’t
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
Watson and Crick’s 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
Go to Netscape and Chime
Antiparallel Polarity
5’ to 3’
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
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
Operons in Bacteria
Exons and Introns in Eucaryotes
DNA
mature RNA
exon 1
exon 2
intron1
intron 2
Ribonucleic acid (RNA)
Essentially single strand of helix so available to self-basepair to generate 3D structures
Types of RNA molecules
ribosomal RNA (rRNA)
transfer RNA (tRNA)
small nuclear RNA (snRNA)
heteronuclear RNA (hnRNA)
messenger RNA (mRNA)
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)
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)
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)
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)
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
Types of RNA molecules
ribosomal RNA (rRNA)
transfer RNA (tRNA)
small nuclear RNA (snRNA)
heteronuclear RNA (hnRNA)
messenger RNA (mRNA)
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)
Biological Information Flow = Central Dogma
TACTGACGAAAA
ATGACTGCTTTT
AUGACUGCUUUU
Met-Thr-Ala-Phe
DNA
RNA
Protein
transcription
splicing (higher organisms)
translation