Organisation and Control of Prokaryotic

and Eukaryotic Genome

ORGANISATION
A. Prokaryotes:
Single DS circular DNA
o Associated with small amount of proteins
Located within nucleoid region
Smaller DNA rings Plasmids
Protein coding genes usually arranged in an operon.
Genes closely packed very few noncoding gaps
B. Eukaryotes:
N!N"!D#NG $%G#!NS&
#ntrons
o 'ithin genes
o Alternate $NA splicing codes for more than one polypeptide
(ransposons
o )etween genes
o Short inverted repeats that flank coding DNA
%.g. GAA Gene AAG
o *ove from one location on genome to another
DNA intermediate+ cutandpaste mechanism
$etrotransposons
Simple Se,uencing Genes -a.k.a. SA(%LL#(% DNA.
o )etween genes
*ost mammals near centromeres
#n Drosophila in /oth centromeres and telomeres.
o *icrosatellites
01 /p2 030445
relatively sta/le2 highly polymorphic DNA markers in linkage mapping.
o *inisatellites
64044 /p2 thousands of times
used in DNA fingerprinting
Pseudogenes
o Genes that have lost function
Due to random mutations
o %volutionary significance
C. Telomeres
*ultiple repetitions of short non-codin nucleotide se,uence
o #n humans2 ((AGGG repeated 04404445
7unction&
o Protects genes from erosion via successive rounds of DNA replication
Telomeres ser!e as "u##ers $sacri#icial %rotection&
To ensure t'at critical %roteins (ill still "e synt'esised in t'e dau'ter
cells des%ite t'e s'ortened c'romosomes.
Cells (ill also undero a%o%tosis a#ter a limited num"er o# cell
di!ision)mitosis $*+& i.e. ('en a critical lent' o# t'e telomere is
reac'ed.
T'is limits t'e e,tent o# accumulated mutations and %re!ents t'e
de!elo%ment o# cancer.
o Prevents fusion of ends with the ends of other chromosomes -chromosomal mutation.
-'ic' can disru%t reulatory control o# enes on t'e ad.oined
c'romosomes
o *aintains integrity of chromosomal ends
)roken chromosomes that lack telomeres recognised as defective /y cellular
DNA repair machinery2 which remedies situation /y putting /roken ends
together2 restoring the telomeres.
#nappropriate repair&
chromosome fusion !$
attracts en8ymes that degrade the chromosome entirely.
/. Centromeres
Appear as constrictions in eukaryotic chromosomes.
%nsure proper segregation of chromosomes&
o 9old sister chromatids together
*itosis& up to /eginning of anaphase
*eiosis& up to anaphase 6
%la/oration of kinetochore -composed of DNA and proteins.
o :inetochore site at which chromosomes attach to the spindle fi/res -/oth during
mitosis and meiosis.
o *otor proteins in kinetochore assist movement of sister chromatids to opposite poles
-during anaphase2 after the centromere holding 6 sister chromatids divides.
0. Gene Am%li#ication
Process of increasing num/er of copies of a gene
6 mechanisms&
o DNA replication
0. Single strand /roken
6. )roken strand replicated dou/le stranded /reak occurs
1. Leads to chromosomal rearrangement2 including gene amplification
o $ecom/ination and segregation
*isalignment and recom/ination /etween sister chromatids
!ne chromatid with a duplicated segment
Another with a deleted segment
7urther rounds of misalignment causes linear amplification of duplicated
segment.
Significance varies with organism
o #n developing South American clawed frog2 simultaneous transcription of amplified
r$NA genes allows ri/osome synthesis to /e completed in ;4 <4 days instead of
0444.
o Association with drug resistance in malignant tumours in mammals.
o Generation of multiple copies of oncogenes in mammals.
"!N($!L
= levels&
(ranscriptional
Posttranscriptional
(ranslational
Posttranslational
Stage Prokaryotes %ukaryotes
(ranscription Promoter
o 9as consensus se,uences
(A(AA( at 04
((GA"A at 13
Sima 0actor
O%eron
Promoter
o (A(A /o> at roughly 63
Transcri%tion 0actors
o ?? re,uired to recognise the (A(A /o> and
to recruit $NA polymerase
Control Elements
o = types&
Promoters
9igh level of transcription& /inding of
transcription factors to control elements
/eyond the promoter on DNA.
Promoter-%ro,imal elements $PPE&
En'ancers
are distal control elements
looping mechanism
Silencers
"ompetitive DNA /inding
*asking activation surface
Direct interaction with the general
transcription factors
Post
(ranscription
m$NA is immediately ready #or translation *1 2-met'yluanosine $2-3G& ca%%in
41 PolyA tail
RNA S%licin
(ranslation mRNA deradation
o degraded /y nucleases after only a
few minutes
initiation o# translation
o antisense $NA
mRNA deradation
o halflives from minutes to months
initiation o# translation
o initiation factors
Post
(ranslation
Co!alent 3odi#ication $In Goli A%%aratus&
P'os%'orylation)/e%'os%'orylation
0eed"ack control
Cyto%lasm Goli A%%aratus
A. Prokaryotes
(ranscription
Promoter
o (wo short se,uence elements within the promoter
Located appro>imately at 13 and 04
o "onsensus se,uences
(A(AA( at 04
((GA"A at 13
Sigma 7actor
o Su/unit of $NA polymerase
o $ecogni8es promoter elements -at /oth 04 and 13.
o Disassociates from polymerase once transcription /egins
o Different sigma factor for different genes
??Specificity ensures only certain genes are transcri/ed only when correct
sigma factor /ecomes availa/le
!peron
o $epressi/le trp operon
o #nduci/le lac operon
Post(ranscription
m$NA is immediately ready for translation
(ranslation
m$NA degradation
o short lifespan
o degraded /y nucleases after only a few minutes
initiation of translation
o antisense $NA
o /inds to m$NA to downregulate its translation
Post(ranslation
"ovalent *odification
o !ccurs in cytoplasm
Pri/now )o>
7or $NA polymerase to /ind to
Phosphorylation@Dephosphorylation
7eed/ack control
B. Eukaryotes
(ranscription
Promoter
o (A(A /o> at roughly 63
(ranscription 7actors
o ?? ($ANS"$#P(#!N 7A"(!$S re,uired to recognise the (A(A /o> and to recruit
$NA polymerase
o vs. prokaryotic sigma factor
o specific in /inding -to proteins2 other transcription factors and control elements.
"ontrol %lements
o a.k.a. cisacting elements
o noncoding DNA se,uences
/ound /y transcription factors to help regulate the transcription of a gene
o = types&
Promoters
/asal level of transcription& transcription factors interacting with $NA
polymerase with promoter.
9igh level of transcription& /inding of transcription factors to control
elements /eyond the promoter on DNA.
Promoterpro>imal elements -PP%.
lies within 044644 /p upstream from start site of transcription and
(A(A /o>
"AA( /o> and G" /o> found within 34 and 044 region
%nhancers
-compared to PP%. are distal control elements
positive regulatory elements+ upregulation of transcription
thousands of nucleotides upstream2 downstream of transcription start or
even within an intron
/ound /y transcription factors known as activators.
7or $NA polymerase to /ind to
looping mechanism
o direct interaction of the activators with the $NA polymerase or
transcription factors at the (A( site upregulates@stimulates
transcription of a gene.
Silencers
DNA elements
#nhi/it gene e>pression
)ound /y transcription factors known as repressors
*echanism&
o "ompetitive DNA /inding
o *asking activation surface
o Direct interaction with the general transcription factors
Post(ranscription -still prem$NA.
3A Bmethylguanosine -B*G. capping
o prevents degradation /y cellular nucleases
o recognition of resultant m$NA /y initiation factors -promoting ri/osome /inding to
initiate translation.
1A PolyA tail
o DNA 04 13 nucleotides /eyond AACAAA se,uence cleaved en8ymatically.
o PolyA polymerase then adds a/out 644 adenine nucleotides to 1A end.
o %nhances sta/ility of m$NA2 impeding degradation /y nucleases
o Direct the transport of m$NA from nucleus to cytoplasm
$NA Splicing
o Spliceosome removes introns2 Doins e>ons
o Earious permutations of splicing
(ranslation
m$NA degradation
o halflives from minutes to months
initiation of translation
o initiation factors
needed to ena/le ri/osomes to attach to the m$NA for initiation of translation
Post(ranslation
"ovalent *odification
o !ccurs at golgi apparatus
Phosphorylation@Dephosphorylation
7eed/ack control