Introduction to Molecular Biology and Genomics

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 Assist[.]

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

 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

000.0E+0 200.0E+6 400.0E+6 600.0E+6 800.0E+6 1.0E+9 1.2E+9 1.4E+9 1.6E+9

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

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

• Computational Biology (Jan-Feb)

– Focus will be modeling approaches and utility of modeling and

simulation of biological systems

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

Minimal Media Add back a single component to minimal

media

Xray mutagenesis

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 con’t

– Chargaff (Columbia again) demonstrates a one

to one ratio of adenine to thymine and guanine

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

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

Operons in Bacteria

Exons and Introns in Eucaryotes

DNA

mature RNA

exon 1 intron1 exon 2 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