4.ModelOrganisms(1)Bacteria (E. coli, several others)(2) Yeast (Saccharomycescerevisiae)(3)Plant (Arabidopsis thaliana)(4) Caenorhabditis elegans(5) Fruit fly(6) Zebrafish(7) Mouse(8)Human2.3FeaturesofGenomicOrganization1.FFeaturesof prokaryoticgenomes(1)Relatively small(2) Simple structure(3) Transcription unit - A segment of DNA that contains signals for the initiationand termination of transcription, and is transcribed into one primary RNAmolecule(4) Overlapping gene -Different genes whose nucleotide coding sequencesoverlapto some extent.The common nucleotide sequenceis read in twoor three different reading frames thus specifying different polypeptides.2.GenomesofProkaryotes(1)E.coliGenome(2))Phagegenome(3)Mu phage3.FeaturesofEukaryoticGenomes(1)Big size, big contentCvalue-Ameasure of the amount of DNA in the haploid genome of an organism,whichcanbebymassorbymolecularweight.14
14 4. Model Organisms (1) Bacteria (E. coli, several others) (2) Yeast (Saccharomyces cerevisiae) (3) Plant (Arabidopsis thaliana) (4) Caenorhabditis elegans (5) Fruit fly (6) Zebrafish (7) Mouse (8) Human 2.3 Features of Genomic Organization 1. Features of prokaryotic genomes (1) Relatively small (2) Simple structure (3) Transcription unit - A segment of DNA that contains signals for the initiation and termination of transcription, and is transcribed into one primary RNA molecule. (4) Overlapping gene - Different genes whose nucleotide coding sequences overlap to some extent. The common nucleotide sequence is read in two or three different reading frames thus specifying different polypeptides. 2. Genomes of Prokaryotes (1) E.coli Genome (2) Phage genome (3) Mu phage 3. Features of Eukaryotic Genomes (1) Big size, big content C value - A measure of the amount of DNA in the haploid genome of an organism, which can be by mass or by molecular weight
Cvalueparadox-The observationthatthe amountof deoxyribonucleic acid inthe haploid genome is not related to its evolutionary complexity.(2)Repetitive sequence·Singlecopy.Moderatelyrepetitivesequence·Highly repetitive sequenceSatelliteDNA-Aportion of DNA in eukaryotes whosedensity differs from that ofthe majority of DNA and that consists of short, repeating sequences ofnucleotide pairs, often found near the region of the centromere.Minisatellites - The size of a minisatellite ranges from 1 kb to 20 kb. One type ofminisatellites is called variable number of tandem repeats (VNTR). Itsrepeat unit ranges from 10-100 bp. They are located in non-codingregions. The number of repeats for a given minisatellite may differbetween individuals. This feature is the basis of DNA fingerprinting.Anothertypeofminisatellites is the telomere.In a human germ cell,the size of a telomere is about 15 kb. In an aging somatic cell, thetelomere is shorter. The telomere contains tandemly repeatedsequence GGGTTA.Microsatellites-Microsatellitesarealsoknownasshorttandemrepeats(STR)becausearepeatunitconsistsofonly1-6bpandthewholerepetitiveregion spans <150 bp. Similar to minisatellites, the number of repeatsfor a given microsatellite may differ between individuals.Therefore,microsatellites can also be used for DNA fingerprinting.(3)>90% of genome is Non-coding sequence, lots of cis-acting elements(4) Single cistron(5)Interrupted gene-exonand intronGT-AG rule (GU-AG rule)- Almost all introns have constant dinucleotide GT(GU) at the first two position and AG at the last two position(6) Pseudogene -An inactive gene derived from an ancestral active gene.A"duplicated”pseudogene arises when a cell is replicating its own DNA andinsertsanextracopyofageneintothegenomeinanewlocation.A"processed"pseudogene is formed during gene expression, when a gene istranscribed into RNA,then that transcript is processed into a mRNA.Normally,the15
15 C value paradox - The observation that the amount of deoxyribonucleic acid in the haploid genome is not related to its evolutionary complexity. (2) Repetitive sequence Single copy Moderately repetitive sequence Highly repetitive sequence Satellite DNA - A portion of DNA in eukaryotes whose density differs from that of the majority of DNA and that consists of short, repeating sequences of nucleotide pairs, often found near the region of the centromere. Minisatellites - The size of a minisatellite ranges from 1 kb to 20 kb. One type of minisatellites is called variable number of tandem repeats (VNTR). Its repeat unit ranges from 10-100 bp. They are located in non-coding regions. The number of repeats for a given minisatellite may differ between individuals. This feature is the basis of DNA fingerprinting. Another type of minisatellites is the telomere. In a human germ cell, the size of a telomere is about 15 kb. In an aging somatic cell, the telomere is shorter. The telomere contains tandemly repeated sequence GGGTTA. Microsatellites - Microsatellites are also known as short tandem repeats (STR), because a repeat unit consists of only 1-6 bp and the whole repetitive region spans <150 bp. Similar to minisatellites, the number of repeats for a given microsatellite may differ between individuals. Therefore, microsatellites can also be used for DNA fingerprinting. (3) >90% of genome is Non-coding sequence, lots of cis-acting elements (4) Single cistron (5) Interrupted gene - exon and intron GT-AG rule (GU-AG rule)- Almost all introns have constant dinucleotide GT (GU) at the first two position and AG at the last two position. (6) Pseudogene - An inactive gene derived from an ancestral active gene. A “duplicated” pseudogene arises when a cell is replicating its own DNA and inserts an extra copy of a gene into the genome in a new location. A “processed” pseudogene is formed during gene expression, when a gene is transcribed into RNA, then that transcript is processed into a mRNA. Normally, the
mRNA is destined for translation into a protein-but sometimes it can instead bereverse-transcribed back into DNA form and inserted in the genome.(7) Organellegenomes(mitochondrialDNA,mtDNA;chloroplastDNA,ctDNA)(8)DNApolymorphism(9)Telomere4.Genomeof Eukaryotes(1) Humangenome(2)Othergenomesof EukaryotesMousegenomeYeast.DrosophilaC. elegansArabidopsis thaliana2.4Nucleosome&Chromosome1.Histones and Non-histone2.Nucleosome(1) Concept-(2) PackingNucleosomes form theprimary level of nuclear DNA compaction in almost alleukaryotes. In all cases, they contain essentially the same four histones, H2A,H2B, H3and H4, always arranged as (H2A+H2B)-(H3+H4)2-(H2A+H2B) heterodimers in anoctamercore,with=200bpofDNA.3.DNACoilingintoaChromosomeDNA (2 nm) + histones → nucleosome (11 nm) → solenoid (30 nm)→chromatinfiber(300nm)→chromatid(700nm)→chromosome(1400nm)16
16 mRNA is destined for translation into a protein—but sometimes it can instead be reverse-transcribed back into DNA form and inserted in the genome. (7) Organelle genomes (mitochondrial DNA, mtDNA; chloroplast DNA, ctDNA) (8) DNA polymorphism (9) Telomere 4. Genome of Eukaryotes (1) Human genome (2) Other genomes of Eukaryotes Mouse genome Yeast Drosophila C. elegans Arabidopsis thaliana 2.4 Nucleosome & Chromosome 1. Histones and Non-histone 2. Nucleosome (1) Concept - (2) Packing Nucleosomes form the primary level of nuclear DNA compaction in almost all eukaryotes. In all cases, they contain essentially the same four histones, H2A, H2B, H3 and H4, always arranged as (H2A+H2B)-(H3+H4)2-(H2A+H2B) heterodimers in an octamer core, with ≈200 bp of DNA. 3. DNA Coiling into a Chromosome DNA (2 nm) + histones → nucleosome (11 nm) → solenoid (30 nm) → chromatin fiber (300 nm) → chromatid (700 nm) → chromosome (1400 nm)
2.5DNAReplication1.Semiconservativereplication(1)Models ofDNAreplication·Semiconservaticvemodel-Semiconservativereplication(Eachstrandactsasatemplateforanewdoublehelix,inwhicheachdouble-strandedmoleculeiscomposedofoneparentalstrandandonenewlypolymerizedstrandConservativemodel?.Dispersivemodela)Semiconservativemodelb)Conservative modelc) Dispersive modelParentalParentalMSAfterfirstAfterfirstAfter firstFreplicationreplicationreplicationcyclecyclecycleMMMMMMAftersecondAfteonnAfterreplicationreplicationreplicationCyolecycleovclePhoto-DNAinDensito-BRIE.coliCsCIDNA90metricculturesgradientcompositionscansbandsStartHeavy15N-containingHENAISN)mediumDNAContinue growing tirstgeneration in14NmediumReplicationHeavy.light.cycle2(hybrid15N/14N)DNAContinuegrowingReplicationScycle3Mean-N)DNA2DNAContinuegrowingReplicationSVVcycle4SSI214N/14N14N/14N15N/14N14N/14N
17 2.5 DNA Replication 1. Semiconservative replication (1) Models of DNA replication Semiconservaticve model - Semiconservative replication (Each strand acts as a template for a new double helix, in which each double-stranded molecule is composed of one parental strand and one newly polymerized strand. Conservative model Dispersive model
(2)Replicationelements·Replicon-Areplicon isa DNAmoleculeorRNAmolecule,ora regionof DNAorRNA,thatreplicatesfromasingleoriginofreplication.·Replicationfork-Thereplicationforkisa structurethatformswithinthenucleus during DNA replication. It is created by helicases, whichbreak thehydrogen bonds holding the twoDNA strands together.Origin (ori)-The origin is a sequence of DNAat which replication is initiated.Prokaryotes have a single circular molecule of DNA, and only asingleoriginofreplicationpercircularchromosome.Eukaryotesoften have multiple origins of replication on each linearchromosome.Terminus:AterminusisasegmentofDNAatwhichreplicationends·Direction:unidirectional,bidirectionalreplication:Replicationspeed2.EnzymesinvolvedinDNAreplication(1)TopoisomeraseI-removessupercoils(2) Helicase-untwistsDNA(3)Single strand binding proteins - stabilize replication fork(4) Primase-makesRNAprimer(5)DNAPolymerase III -synthesizesnewDNAstrands(6)DNApolymeraseI-removesRNAprimer,addsDNAbases(7)DNA ligase-seals lagging strand 3'open holesRNADNA polymerase IIIprimerLaggingstrandOkazakifragmentTemplateDNA2SSBproteinDNAprimas5'ParentalX3'DNADNAhelicaseDirection of forkmovement5CDNApolymeraseIIITemplateLeadingDNAstrand18
18 (2) Replication elements Replicon - A replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication. Replication fork - The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. Origin (ori) - The origin is a sequence of DNA at which replication is initiated. Prokaryotes have a single circular molecule of DNA, and only a single origin of replication per circular chromosome. Eukaryotes often have multiple origins of replication on each linear chromosome. Terminus: A terminus is a segment of DNA at which replication ends. Direction: unidirectional, bidirectional replication Replication speed 2. Enzymes involved in DNA replication (1) Topoisomerase I - removes supercoils (2) Helicase - untwists DNA (3) Single strand binding proteins - stabilize replication fork (4) Primase - makes RNA primer (5) DNA Polymerase III - synthesizes new DNA strands (6) DNA polymerase I - removes RNA primer, adds DNA bases (7) DNA ligase - seals lagging strand 3' open holes