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Organisation and Control of Prokaryotic and Eukaryotic Genome

Saturday, 21 June 2014

11:29 AM

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Features

Prokaryotes

Eukaryotes

Gene Length

Shorter

Longer

Genome Size

Smaller

Larger

Amount of Non- Only a small amount is nonCoding DNA
coding
• Regulatory sequences
such as promoters or
operators

>90% is non-coding
• Introns, satellite DNA, control elements

Form/Shape

Single, circular chromosome

Multiple, linear chromosomes

Coding
sequences
along gene

Continuous

Interrupted by non-coding introns in-between exons

Plasmids

Smaller circular mitochondria and chloroplast DNA

Organisation of In operons
related genes
Genes share common
promoter and operator

Operons absent
Genes have independent promoters, and hence may not be regulated
together

Packing of DNA Folded into looped domains,
held together by protein
scaffolds

Packaged into chromatin, which is made up of nucleosomes, loops of DNA
wound around an octamer of histone proteins
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Describe the structure and function of the portions of eukaryotic DNA that do not encode for protein or RNA, with
reference to intron, centromere, telomere, promoter, enhancer and silencer
...
)
Non-coding Sequence Definition
Introns
Promoter

• Found within eukaryotic genes
• Plays a role in alternative splicing

• Specific site where RNA polymerase attaches to initiate transcription of mRNA

Enhancer

• Specific site that can activate transcription of a gene from thousands of base pairs away

Silencer

• Specific site that can suppress transcription of a gene from thousands of base pairs away

Centromere

• Constricted regions of the chromosome composed of highly repeated sequences
Bio Notes Page 1

Centromere

• Constricted regions of the chromosome composed of highly repeated sequences

Telomere

• A repeated DNA sequence forming the ends of linear DNA

Satellite DNA

• Functions in sister chromatid adhesion and kinetochore formation

• Protects the gene from being eroded from successive rounds of replication
• Determines the lifespan of a cell

• Short repetitive DNA sequences in tandem arrays
• Minisatellites (VNTR)
• Microsatellites
• May be polymorphic, used in DNA fingerprinting

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○ Centromeres
 A constricted regions of the chromosome composed of highly repeated sequences
 Functions in sister chromatid adhesion and kinetochore formation
□ The kinetochore is a complex of proteins that serve as the attachment point for spindle fibres
 Aberrant centromere function can lead to improper chromosomal alignment and segregation, resulting in nondisjunction of chromatids (Aneuploidy)
○ Telomeres
 A repeated DNA sequence forming the ends of linear DNA
 Protects the gene from being eroded from successive rounds of replication
□ To prevent the loss of crucial genes
□ Due to end replication problem
 DNA polymerase requires a free 3'OH end to add nucleotides to
 At the end of the last Okazaki fragment, there is no 3'OH end to add nucleotides to
 The newly formed daughter stand is shorter than the parental strand
 With each replication, the stand gets shorter and shorter, and critical genes may be lost
 Maintains the integrity of the chromosome ends
□ Prevent fusion of chromosomal ends, which could disrupt regulation on adjoined chromosomes
 Prevent DNA repair machinery from recognising and sticking together the ends
 Limits the lifespan of the cell
□ Triggers apoptosis
□ Limits the extent of accumulated mutations and prevents the development of cancerous cells
 Can be extended by telomerase

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○ Gene amplification is a process in which multiple copies of a specific gene or genes are produced so as to increase the
number of DNA templates, which in turn increases the quantity of gene products
 Results from repeated replication of DNA in a limited portion of the genome
○ This offers an alternative method for control of gene expression, and may be developmentally or environmentally
regulated
○ Can be found as free extra-chromosomal molecules (double minute chromosomes in cancer) or as tandem arrays
within a chromosome
Area of
Significance

Amplification
of rRNA in
amphibians
(embryos)

Significance

Process

• High requirements for protein synthesis for
embryonic growth

• At origin of replication of extra-chromosomal
circular DNA molecules containing rRNA genes,
a nick is made at one strand, exposing free 3'OH
• Requires huge number of ribosomes for protein end
synthesis → Requires high rate of transcrip on
of rRNA → Exis ng number of genes cannot be
transcribed rapidly enough; Amplification of
genes required

Bio Notes Page 2

• DNA polymerase adds to the 3'OH end → new
stand synthesised using un-nicked strand as
template
• 5' end of the nicked strand becomes displaced
→ displaced linear, single-stranded DNA used as
template for DNA polymerase to replicate
discon nuously → new DNA containing mul ple
copies of rDNA genes

Amplification
of genes
coding for
chorion in
Drosophila

• High requirements for chorion proteins for
production of eggshell during oogenesis
• Amplification of region beyond the immediate
regions of the genes involved with chorion
production

Multiple initiation of DNA replication

• Chorion genes found near origin of
replication
• Helicase binds to ori and unwind DNA,
initiating replication
• Before first round of replication, helicase
binds to new ori and initiates second round
of replica on → replica on bubble formed

Drug resistance Genes are amplified via
in tumour cells
• Amplification of genes inhibited by drugs
○ Due to aneuploidy of cell + further
amplification later
○ Overwhelm ability of drugs to control
malignant growth
Conversion of
protooncogenes to
oncogenes
Gene
amplification in
evolution and
diversity

Breakage-fusion-bridge cycle

• Accidental DNA damage to gene coding for
p53 protein → p53-defective cell enters S
phase → sister chroma ds produced
without telomeres → fusion of chroma ds
by DNA repair mechanisms → unequal
breakage during anaphase

• Amplification of MDR genes

○ Protein product of MDR gene acts as
a pump → selec vely eject drug
molecules from cell

• Some ampificated products present as
Bio Notes Page 3

• Repeated rounds of replication, chromatid
fusion and unequal breakage result in
accumulation of genes in duplicated region

diversity

• Some ampificated products present as
double minutes → extrachromosomal
structures

accumulation of genes in duplicated region

Through amplifica on of oncogenes →
deregulated cell growth

• myc oncogene gene in most cancers

• ErbB or HER-2/neu oncogene in breast and
ovarian cancer
Natural selection selects for organisms with
advantageous phenotypes
• Extra amplified copies of genes less
subjected to natural selec on →
accumulates random muta ons →
divergence; increases gene pool of
population

• Slippage and subsequent reattachment of
DNA polymerase → bubble formed in new
strand

• DNA repair mechanisms realign the
template stand with the new stand to
straighten out the bubble → expanded
section is amplified

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Intron Splicing

Excision of non-coding introns and spicing of coding exons together by spliceosomes to
form mature mRNA
• Allows fro alternative splicing of mRNA to give different protein products

Polyadenylation of 3'OH Poly-A tail of 50-200 adenine nucleotides is added to 3'OH end of mRNA by nuclear
end
polymerases
5' Capping

7-methylguanosine residue added to 5' end of pre-mRNA

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g
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Histone
Acetylation of the free lysine residues at N-terminus end of histone
Acetylation molecules → decrease in net posi ve charge → lower affinity for
negatively-charged DNA phosphate backbone → chroma n thread
become less condensed

• Allows greater accessibility to
DNA

DNA
Methylation of CPG-rich sites
Methylatio
n
• Interferes with binding of transcription factors

• Reinforces transcriptional
repression and gene silencing

Bio Notes Page 4

• Facilitates assembly of
general transcription factors
and DNA polymerase at
promoter

• Interferes with binding of transcription factors
• Induces histone acetylation

Location

Promoter

Type of
General
Transcription Transcription
Factor
Factors
Functions

Specific Transcription Factors:

Specific Transcription Factors:
Repressors

Distal to gene undergoing transcription

Distal to gene undergoing
transcription

1
...
Looping mechanism brings specific
1
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Formation of
(TIC)
complex
transcription
initiation complex
3
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Allows activator-enhancer complex to 2
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State the various ways in which gene expression may be controlled at translational (e
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half life of RNA, 5′ capping,
initiation of translation) and post-translational level (e
...
biochemical modification and protein degradation)
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Translational
Half-life of mRNA • Length of poly-A tail

• Binding of specific proteins to 3'UTR
• Hormones

• Longer the poly-A tail → more stability against
degradation by exonucleases
• Specific proteins mark the mRNA for rapid
degradation
• May stimulate or retard the rate of degradation

5' capping

Initiation of
Translation

• Stabilises mRNA against degradation from
5'exonucleases

Masking using repressor proteins to
bind to 5'UTR of mRNA
Bio Notes Page 5

Steric hindrance → prevent ribosome binding →
decreases rate of translation

Translation

bind to 5'UTR of mRNA

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Outline the differences between prokaryotic control of gene expression with the eukaryotic model

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