Genes and DNA

Picture:C.WilliamBirky,Jr.DepartmentofEcologyandEvolutionaryBiology.TheUniversityofArizona

Genes
Whatisgene?
a) Onegeneoneenzyme.
b) Onegeneoneprotein(polypeptide).
c) GenesaresegmentsofDNAthatcodefor
polypeptidesandRNAs.
Answer...

Experimental procedures demonstrating that DNA is the genetic material

1940s

ProofthatDNAistheGenetic
Material
HersheyandChase
Usedviralparticles(phages)
Determinedgeneticmaterialwascontainedin
DNAratherthanproteincoat

Genes are DNA

Flourescence micrograph
of alga Olisthodiscus
(Alga). Chlorophyll
autofluoresces red. DNA
stained with DAPI
fluoresces white.
Chloroplasts and cpDNA
Mitochondria and mtDNA
Nucleus and nuDNA

GenesareDNA
Geneticinformationiscarriedinthelinear
sequenceofnucleotidesinDNA
Geneticinformationcontainsinstructionsto
synthesizeproteins

Some Definitions
A gene is a segment of a DNA molecule
(or RNA in some viruses).
OccurinPairsgenesfoundonhomologous
chromosomesinsomaticcells(diploid)
Dominantgenethatisalwaysexpressed
RecessivegenethatisexpressedONLYif
2arepresent

Some Definitions
The phenotype of a cell or organism
is determined jointly by the
organisms genotype and
environment.
The genotype consists of the genes
that control the trait of interest.
Codominantbothgenesarealwaysexpressed

Some Definitions
The genome of an organism is
(i) the sum of all of the DNA in one set
of chromosomes (broad sense);
(ii) the sum of all of the genes in one set
of chromosomes (narrow sense).

Genes and Chromosomes in

Eukaryotes

Human DNA in one genome

It is divided into 23 chromosomes.
Somatic cells have two sets of 23
chromosomes.

Genes and Chromosomes in Bacteria

gene1gene2gene3

Electron micrograph
Very small circular DNA

Structure of DNA : determined

by Watson and Crick in1953
DNA and its Building
Nucleotides:
Guanine (G), Adenine (A),
Cytosine (C), Thymine (T).
Polarized strand : 5->3
Base inside, sugar outside

 Whataresomeoftheimportantstructuralfeaturesof
theDNAdoublehelix?

TheProblem
Humangenome(indiploidcell)=6x109bp
6x109bpx0.34nm=2.04x109nm=2m/cell
Verythin(2.0nm)extremelyfragile
Diameter of nucleus = 5 10 m

DNAmustbepackedtoprotectit,butstillbe
accessibletoallowgeneexpressionandcellular
responsiveness

DNA Structure: The Final

Simplification
A gene is a sequence of bases in one strand
of DNA.
3'OHdRPdRPdRPdRP5'
|||
|
TCG
A
..
........

A
GCT
|||
|
5'PdRPdRPdRPdROH
3

3TCGA
5AGCT

Genesequencescanbewrittendown
andreadlikeanytext
Presentedhereisthesequenceof
nucleotidesinthehumanglobingene
Thethreeregionsofthegenethatspecify
theaminosequencefortheglobinprotein
(EXON)

Human -globin Gene Determines

Amino Acid Sequence of -globin
1102030405060708090100
AcatttgcttctgacacaactgtgttcactagcaactcaaacagacaccATGGTGCACCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGC
101
AAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGgttggtatcaaggttacaagacaggtttaaggagaccaatagaaactgggcatgtggag
201
acagagaagactcttgggtttctgataggcactgactctctctgcctattggtctattttcccacccttagGCTGCTGGTGGTCTACCCTTGGACCCAGA
301
GGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGA
401
TGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGgtgagt
501
ctatgggacccttgatgttttctttccccttcttttctatggttaagttcatgtcataggaaggggagaagtaacagggtacagtttagaatgggaaaca
601
gacgaatgattgcatcagtgtggaagtctcaggatcgttttagtttcttttatttgctgttcataacaattgttttcttttgtttaattcttgctttctt
701
tttttttcttctccgcaatttttactattatacttaatgccttaacattgtgtataacaaaagcaaatatctctgagatacattaagtaacttaaaaaaa
801
aactttacacagtctgcctagtacattactatttggaatatatgtgtgcttatttgcatattcataatctccctactttattttcttttatttttaattg
901
atacataatcattatacatatttatgggttaaagtgtaatgttttaaaattttgcatttgtaattttaaaaaatgctttcttcttttaatatactttttt
1001
gtttatcttatttctaatactttccctaatctctttctttcagggcaataatgatacaatgtatcatgcctctttgcaccattctaaagaataacagtga
1101
taatttctgggttaaggcaatagcaatatttctgcatataaatatttctgcatataaattgtaactgatgtaagaggtttcatattgctaatagcagcta
1201
caatccagctaccattctgcttttattttatggttgggataaggctggattattctgagtccaagctaggcccttttgctaatcatgttcatacctctta
1301
tcttcctcccacagCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGT
1401
GGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAgctcgctttcttgctgtccaatttctattaaaggttcctttgttccctaagtccaac
1501
tactaaactgggggatattatgaagggccttgagcatctggattctgcctaataaaaaacatttA

Many eukaryotic genes contain intervening

sequences (introns)

Many eukaryotic genes contain

intervening sequences (introns)
Genesvarygreatlyinsizeandintron/exon
organization.
Somegenesdonthaveanyintrons.Most
commonexampleisthehistonegenes.

Howdoesgenesfunction?
CentralDogma:DNAtoRNAtoProtein.

DNA to Protein

Cell Nucleus
Compartmentalized DNA activity
Nuclear pores allow communication
Nuclear lamina and cytoskeleton
mechanically support the nucleus

Nucleus

Whatkindsofmoleculesaretransportedacrossthe
nuclearenvelope?

Genes
Probablyabout3000035000genes
Genedensityvariesalongchromosomes
genesaremostlyineuchromatin,
notintheheterochromatinnearthe
centromeresorontheshortarmsof
acrocentricchromosomes.

Genes
Mostgenes(9095%probably)codefor
proteins.
ThereareasignificantnumberofRNA
onlygenes

ProteincodingGenes
Somegenesarequitehuge:
dystrophin(associatedwithDuchennemuscular
dystrophy)is2.4Mbpandtakes16hourstotranscribe.
Morethan99%ofthisgeneisintron(totalof79introns).
Mostexonsareshort:200bponaverage.
Intronsizevarieswidely,fromtenstomillionsofbase
pairs.

However,highlyexpressedgenesusuallyhaveshortintrons

RNAGenes

ThebestknownRNAgenesare
ribosomalRNAandtransferRNA
genes.

RibosomalRNAgenes:The
nucleolussitsonthesegenes,
whicharesometimescalled
nucleolusorganizerregions.

TransferRNAgenesare
dispersedthroughoutthegenome,
usuallyinsmallclusters.There
are49familiesoftRNAgenes.

OtherRNAGenes
SmallnuclearRNA(snRNA)andsmall
nucleolarRNA(snoRNA)genesfor
ribozymes(catalyticRNAmolecules)which
areinvolvedwithRNAsplicingandRNA
basemodification.
Alsogenesfortelomerase,signal
recognition,Xchromosomeinactivation,
imprinting,andprobablyquiteabitelse.

OtherRNAGenes
MicroRNAs(miRNA)andsmallinterferingRNAs
(siRNA)regulatetranslationofspecificmRNAs
miRNAseemstohavearoleindevelopment.
siRNAisabasisforapopulartechniquecalled
RNAinterference,whichallowsspecificgenes
tobeinactivated.

Agenecluster
Ageneclusterisasetoftwoormoregenes
thatservetoencodeforthesameorsimilar
products.
AnexampleofageneclusteristheHuman
globingenecluster,whichcontainsfive
functionalgenesandonenonfunctional
genewhichcodeforsimilarproteins.

Betaglobingenecluster
thebetaglobincluster,which
contains5verysimilargenes.

All play the beta role in

hemoglobinmolecules(22),
but in different ways: beta is
part of HbA, 99% of adult
hemoglobin; delta is part of
HbA2, 1% of adult
hemoglobin; the two gamma
genes (almost identical) are
part
of
HbF,
fetal
hemoglobin;epsilonispartof
embryonichemoglobin..

GenomicDNA

humangenome
alltheDNApresentinthecell.
thenucleargenome(about3200Mbp)andthe
mitochondrialgenome(16.6kb).
thatnuclearDNA:auniquefractionandseveral
classesofrepeatedsequenceDNA.

Typesofsequencesinthehumangenome

LINEs(longinterspersednuclearelements),
SINEs(shortinterspersednuclear
elements),
Microsatellites(SSRs)aremuchshorter,2
5bprepeats,andmicrosatellitearraysare
foundalloverthegenome.

ProkaryoticChromosome
Manyprokaryotescontainasinglecircular
chromosome.
Prokaryoticchromosomesarecondensedin
thenucleoidviaDNAsupercoilingandthe
bindingofvariousarchitecturalproteins.

DNASupercoilingin
Prokaryotes

anE.colicell
AsingleDNAmoleculecontaining
over4.6millionbasepairs
encodingapproximately4,300
genes.
Thesmallcircletsareplasmids.

ProkaryoticChromosome
BecauseprokaryoticDNAcaninteractwith
thecytoplasm,transcriptionandtranslation
occursimultaneously.
Mostprokaryotescontainonlyonecopyof
eachgene(i.e.,theyarehaploid).

ProkaryoticChromosome
Prokaryoticgenomesareefficientand
compact,containinglittlerepetitiveDNA.
noncodingsequencesaccountforan
averageof12%oftheprokaryoticgenome,
asopposedtoupwardsof98%ofthe
geneticmaterialineukaryotes(Ahnertet
al.,2008)

Prokaryoticplasmids
extrachromosomalDNAmolecules
linearorcircular
typicallysmaller(i.e.,lessthan1,500
kilobases)
encodenonessentialgenes(aidgrowthin
specificconditionsorencodeantibiotic
resistance

Prokaryoticplasmids
Plasmidsreplicateindependentlyoftherest
ofthegenome.
someplasmidsarecapableofintegrating
intochromosomesormovingfromcellto
cell.
haveasingleoriginofreplication

Mostprokaryoticgenomes
areorganizedintopolycistronicoperons,or
clustersofmorethanonecodingregion
attachedtoasinglepromoter,separatedby
onlyafewbasepairs

The lac operon of E. coli

The lac operon of E. coli is a segment of DNA that includes a promoter, an operator, and the three structural genes
that code for lactose-metabolizing enzymes.
2008 by Sinauer Associates, Inc. All rights reserved. Used with permission.

TheretrovirusgenomeisRNAWhenitentersacell,theRNAgets
translatedtoformreversetranscriptase,whichcopiestheviralRNA
intoDNA.
ThisDNAthenintegratesintothegenome:itbecomesaprovirus.The
provirusDNAistranscribedtomakemoreviralRNAsandproteins.
Thevirusbudsoutthroughthecellmembrane.
Basicstructureofretrovirus:3genes
gag:RNAbindingproteins(viruscore)
pol:reversetranscriptaseandotherprocessingenzymes
env:outercoatprotein

Chromosomes
Whatischromosome?
ChromosomeisacomplexofDNA,RNAand
proteins.Eachchromosomeconsistsofone
DNAmolecule.

Chromosomesbecomevisibleas
cellspreparetodivide

HeterochromatinandEuchromatin

Extremecondensationsilences
expression
Heterochromatin

Darklystainedregionofchromosome
Highlycompactedevenduringinterphase
Usuallyfoundinregionsnearcentromere
Constitutiveheterochromatinremainscondensedmostof
timeinallcells(e.g.,Ychromosomesinfliesandhumans)

Euchromatin
Lightlystainedregionsofchromosomes
Containsmostgenes

Heterochromatinversuseuchromatin
Heterochromatinis
darklystained
Euchromatinis
lightlystained
Cbanding
techniquesstains
constitutive
heterochromatin
nearcentromere
Fig.

Chromosomesineukaryotesand
prokaryotesaredifferent
PROKARYOTES
single chromosome plus plasmids

EUKARYOTES
many chromosomes

circular chromosome

linear chromosomes

made only of DNA

made of chromatin, a
nucleoprotein (DNA coiled
around histone proteins)

found in cytoplasm

found in a nucleus

copies its chromosome and divides copies chromosomes, then the

immediately afterwards
cell grows, then goes through
mitosis to organise
chromosomes in two equal
groups
2007PaulBillietODWS

ThelocationofDNAinprokaryotic
cells.
a.nucleus
b.mitochondria
c.cytoplasm
d.vacuole

DNAPROKARYOTES
Isthefollowingsentencetrueorfalse?
Mostprokaryotescontainasingle,circular
DNAmolecule.

DNAEUKARYOTES
EurkaryoticDNAisgenerallylocatedinthe
cell_____intheformofanumberof
chromosomes.

Isthefollowingsentencetrueor
false?
Allorganismshavethesamenumberof
chromosomes.

Whentransformationwasfirstdiscoveredinbacteriaduring
the1940sitsinvestigationbyAveryprovedthat:

a)bacterialculturescanformtumorslikeanimalcells
b)pureDNAcarriesgeneticinformation
c)DNAplusproteinisneededtotransfergenesfrom
onebacterialcelltoanother
d)mutationsoccurspontaneouslythatconvert
harmlessbacteriaintodangerousvirulentstrains
e)bacteriaoftwodifferenttypesmustbemixed
togetherforgenetransfertooccur

Next we will review

how genes
replicate