DNA Structure & Function (Outline)

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DNA Structure & Function (Outline)1. Historical perspective (DNA as the genetic material): Genetic transformation and DNADNA is the genetic material in bacterial viruses (phage)The base-pairing ruleDNA structure2. Basis for polarity of SS DNA and anti-parallelcomplementary strands of DNA3. DNA replication models4. Mechanism of DNA replication: steps and molecularmachinery5. Replication and the end of linear chromosomesMolecular basis for aging6. Fidelity of DNA replication

By definition the geneticmaterial of must be replicatedDNA Replication direct the cell functions byproviding information forproduction of proteinsFlow of the genetic information(Gene Expression)

DNA as the Genetic MaterialTime-line1850’s1870-1890190220th centuryMendelMicrosocopy: Mitosis and MeiosisChromosome basis of inheritance(Thomas H. Morgan)Work with bacteria and viruses

DNA StructurePrior to the 1950s,DNA is a polymerof nucleotidesconsisting of: a nitrogenous base a sugar a phosphate group

1928 Fredrick Griffith ExperimentsConcept of transformation (using Bacteriathat cause pneumonia in mammals)1944 Avery, McCarty, and MacLeodThe transforming material is DNA“DNA is the genetic material”1952 Hershey and ChaseDNA is the genetic material in viruses thatinfect bacteria

Griffith- Phenomenon of Transformation, a change ingenotype (genetic makeup) by a foreign substance thatchanges the phenotype (observed properties) of the cell

History of DNAAvery, MacLeod, and McCarty, 1944- DNA is the transforming material(Can convert Type R bacteria into S)

A phage, is a virus that infects bacteria and ismade of DNA and protein. Alfred Hershey and Martha Chase- thegenetic material of the phage T2 is DNA.Hershey Chase /sites/0072437316/student view0/chapter14/animations.html#

Biochemical analysis of DNA:Base-pairing rule1947 Erwin Chargaff, analysis of DNA from differentspecies %A %T & %C %GHuman DNAA 30.9%T 29.4%C 19.9%G 19.8%Class TP question

Base-pairing in DNA

Structural Model of DNAMaurice Wilkins and Rosalind Franklin- X-raycrystallography: Polynucleotide Helix(a) Rosalind Franklin(b)Franklin’s X-ray diffractionPhotograph of DNA

Watson and Crick deduced that DNA was adouble-stranded helixThrough observations of the X-ray crystallographic images of DNA

Chemical Structure of DNA HHMIPolarity and antiparallel nature ofthe two DNAstrands (5’ and3’ ends)

Watson and Crick- Specificity of pairing is dictated by the structure ofthe basesExample

Three models for DNA replication:Conservative modelSemi-conservative modelDispersive model

Meselson-Stahl ExperimentBacteriacultured inmediumcontaining15NDNA samplecentrifugedafter 20 min(after firstreplication)Bacteriatransferred tomediumcontaining14NDNA samplecentrifugedafter 40 min(after secondreplication)Meselson-Stahl Experiment animationLessdenseMoredense

The Basic concept of DNA replicationEach strand of DNA act as a template forsynthesis of new complementary strands

Major Events in the History of EarthRole of RNA in DNA ReplicationCenozoicHumansLand plantsOrigin of solarsystem deukaryotes41Proterozoic- Archaeaneoneon23ProkaryotesAtmosphericoxygenRNA

Molecular Mechanism of DNA ReplicationCollective action of several macro-molecules: DNA Proteins (enzymes & others) RNA Ribo-protein (for linear chromosomes)Direction of replication of new strands; 5’-----3’How nucleotides are added in DNA replication (Activelink)

DNA polymerase adds deoxyribonucleotides in a 5’ to 3’direction, it adds nucleotides to the 3′ end of a growingstrand.The new strand always starts with the 5’ end, the templatestarts with the 3’ end.

Primase, an RNA polymerase, uses the DNAtemplate strand to polymerize a shortcomplementary RNA chain (RNA primer)Two different DNA polymerases both- cannot initiate the synthesis of a polynucleotide- can only add nucleotides to an existing 3′ end

Summary of DNA ReplicationSemi-conservativeInitiation: Origin of replicationPrimase and RNA primerTemplate strand vs. new strand5’ to 3’ directionDNA polymerase (III and I)Base-pairing rulesdNTPs: deoxy-ATP, deoxy-GTP, deoxy-CTP, deoxyTTPLeading and lagging strandsOkazaki fragmentsDNA ligaseBidirectionalFidelity of DNA replication is maintained by activity ofDNA polymerase and other proof-reading systems.

Origin of ReplicationDNA Replication Tutorial (active link)

Other proteins participate in DNA replicationincluding: Helicase, topoisomerase, singlestrand binding protein

Replication of long DNA molecules begins atmultiple origins of replication simultaneouslyand is bidirectional

Replicating the Ends of linear DNA MoleculesMechanism ofDNA replicationcausestelomeres to getshorter with eachround ofreplicationLast fragmentLagging strand 5′Previous fragmentRNA primer3′Primer removed butcannot be replacedwith DNA becauseno 3′ end availablefor DNA polymerase3′Removal of primers andreplacement with DNAwhere a 3′ end is available5′Second roundof replication5′New leading strand ancer/images.htmlNew leading strand 5′3′Further roundsof replicationShorter and shorterdaughter molecules

Current ConnectionstoDNA structure and replicationQ: Why are we mortal with a limited lifespan?A: Our cells have a limited life span (# of celldivisions)

Telomerase- an enzyme(riboprotein) that extends the3’ end of the DNA strand byadding a repeated sequenceof 6-nucleotides typicallyTTAGGG (100-1000 times)https://www.youtube.com/watch?v AJNoTmWsE0shttps://www.youtube.com/watch?v vtXrehpCPEE

Ends of linear chromosomes have special DNAsequences and are known as telomeresadded by an enzyme known as telomeraseafter DNA replication is completed

Life span of dividing cells Telomerase is active in sperm, eggs, stem cells (bonemarrow), and cancer cells but not in somatic tissuesMost cells lose 50-200 endmost bases after each celldivisionAfter about 50 divisions, shortened telomeres signal thecell to stop dividingFigure 2.3

Fidelity of DNA replication & maintaining DNAintegrityMaintained by:1. Proof-reading function of DNA polymerase2. DNA repair smatch repair-lg.movDNA damage and repair in generalhttp://www.youtube.com/watch?v y16w-CGAa0Y&feature relatedhttp://www.youtube.com/watch?v nPS2jBq1k48

Genetic Integrity and Diversity Need for maintaining genetic integrity isbalanced by having enough geneticvariability for natural selection to act on Few errors of DNA replication are notcorrected!

Genetic transformation and DNA DNA is the genetic material in bacterial viruses (phage) The base-pairing rule DNA structure. 2. Basis for polarity of SS DNA and anti-parallel complementary strands of DNA 3. DNA replication models 4. Mechanism of DNA replication: steps and molecular machinery

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