genomes in prokaryotes and eukaryotes
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GENOMES IN PROKARYOTES AND
EUKARYOTES.
DR KITYAMUWESI RICHARD
MDENT(ORAL AND MAXILLO-FACIALSURGERY)
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GENOMES
Genome is the total genetic information of an
organism.
For most organisms, it is the complete DNAsequence.
For RNA viruses, the genome is the complete
RNA sequence, since their genetic information
is encoded in RNA.
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THE GENOMES OF PROMINENT
ORGANISMS.ORGANISM GENOME SIZE (Mb) GENE NUMBER
Hepatitis B virus 0.0032 4
HIV-1 Virus 0.0092 9
E.Coli 4.6 4437
S.cerevisiae(yeast) 12 6300
D.melanogaster(fruit fly) 137 14000
Homo sapiens(human) 3000 20000-30000
1 Mb = 1 million base pairs (for double-stranded DNA or RNA) or 1 million bases (forsingle-stranded DNA or RNA).
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GENOMES IN EUKARYOTIC CELLS.
Nuclear DNA
Mitochondrial DNA
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NUCLEAR DNA
Consists of chromosomes which are
essentially molecules of DNA.
DNA is a polymer of nucleotides. Genes are located on chromosomes.
Higher organisms have duplicate copies of
each gene hence are called diploid. Diploid cells have two copies of each
chromosome.
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DNA STRUCTURE
In a solution with higher salt
concentrations or with alcohol
added, the DNA structure maychange to an A form, which is still
right-handed, but every 2.3 nm
makes a turn and there are 11 base
pairs per turn.
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DNA STRUCTURE
Another DNA structure is called the Z form because
its bases seem to zigzag. Z DNA is left-handed. One
turn spans 4.6 nm, comprising 12 base pairs. The
DNA molecule with alternating G-C sequences inalcohol or high salt solution tends to have such
structure
DNA exists in a super coiled state largely due to the
action of the enzymes gyrases and topoisomerases .
This is for efficient packing during cell division and in
order to control of expression of parts of the
genome.
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THE NORMAL RIGHT-HANDED "DOUBLE HELIX"
STRUCTURE OF DNA, ALSO KNOWN AS THE B FORM.
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CHROMATIN
Chromatin is the substance which becomes visible chromosomes during prophase of celldivision. Its basic unit is nucleosome,
composed of 146 bp DNA and eight histoneproteins. The structure of chromatin is dynamically changing, at least in part, depending on the need of transcription.
At other times, the chromatin is less condensed, with some regions in a "Beads-On-a-String" conformation.
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CHROMATIN
The 30 nm chromatin fiber is associated withscaffold proteins (notably topoisomerase II) to formloops. Each loop contains about 75 kb DNA. Scaffold
proteins are attached to DNA at specific regions called scaffold attachment regions (SARs), which arerich in adenine and thymine.
The chromatin fiber and associated scaffold proteins coil into a helical structure which may be observed as a chromosome. G bands are rich in A-T nucleotidepairs while R bands are rich in G-C nucleotide pairs.
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STRUCTURE OF CHROMATIN
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STRUCTURE OF NUCLEOSOMES
Histones are the proteins closelyresponsible for the structure of chromatin and play important roles in
the regulation of gene expression. Fivetypes of histones have been identified:H1 (or H5), H2A, H2B, H3 and H4.
H1 and its
homologous
protein H5 areLinker histones they stabilize the solenoidstructure of chromatin.
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STRUCTURE OF NUCLEOSOMES
The other four types of histones associate withDNA to form nucleosomes. H1 (or H5) has about 220 residues. Other types of histones are
smaller, each consisting of 100-150 residues. Each nucleosome consists of 146 bp DNA and 8
histones: two copies for each of H2A, H2B, H3and H4. The DNA is wrapped around thehistone core, making nearly two turns pernucleosome.
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3-D STRUCTURE OF A NUCLEOSOME
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GENERAL ORGANISATION OF DNA
SEQUENCE
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DNA STRUCTURE
A typical DNA molecule consists of genes,pseudogenes and extragenic region.
Pseudogenes are nonfunctional genes. They
often originate from mutation of duplicatedgenes .
Because duplicated genes have several copies, the organism can still survive even if a couple of them become nonfunctional.
Only the exons encode a functional peptide orRNA. The coding region accounts for about 3% of the total DNA in a human cell.
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GENES
A gene is a unit of genetic information thatprovides instruction for a particular propertyof an organism.
It includes the entire nucleotide sequencenecessary for the expression of its product(peptide or RNA).
Each gene may exist in alternative forms calledalleles.
A gene is the fundamental unit of heredity.
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GENE STRUCTURE.
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GENE STRUCTURE.
A gene sequence may be divided intoregulatory and transcriptional regions.
The regulatory region could be near or far
from the transcriptional region.
The transcriptional region consists of exonsand introns.
Exons encode a peptide or functional RNA. Introns will be removed after transcription by
splicesomes and self-splicing.
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ORGANELLE DNAS
Present within the mitochondria of
eukaryotes.
Present within the chloroplasts of plants. These are the main sites of ATP formation
during oxidative phosphorylation.
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HUMAN MITOCHONDRIAL DNA
(eukaryotic cell)
Is much less than in the nuclear genome.
Is a double stranded circular molecule
containing 16,569 base pairs. Encodes for 13 protein subunits that are
associated with proteins encoded by nuclear
genes to form 4 enzyme complexes , 2 rRNAs
and 22 tRNAs needed for protein synthesis by
intramitochondrial ribosomes.
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HUMAN MITOCHONDRIAL DNA
(eukaryotic cell)
There is no effective DNA
repair system in the
mitochondria hence mutations
occur.
Is maternal in origin.
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Mitochondria Contain Multiple mtDNA
Molecules
Individual mitochondria are largeenough to be seen under the light
microscope and even themitochondrial DNA (mtDNA) can bedetected by fluorescence
microscopy. The mtDNA is located inthe interior of the mitochondrion, the region known as the matrix.
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Mitochondria Contain Multiple mtDNA
Molecules
All the mitochondria in eukaryoticcells contain multiple mtDNA
molecules. Thus the total amount of mtDNA in a cell depends on thenumber of mitochondria, the size of
the mtDNA, and the number of mtDNA molecules permitochondrion
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MITOCHONDRIAL GENES
All proteins encoded by mtDNA are synthesizedon mitochondrial ribosomes. All mitochondriallysynthesized polypeptides identified thus far (with
one possible exception) are not completeenzymes but subunits of multimeric complexes used in electron transport or ATP synthesis. Mostproteins localized in mitochondria, such as the
mitochondrial RNA and DNA polymerases, aresynthesized on cytoplasmic ribosomes and areimported into the organelle .
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Products of Mitochondrial Genes Are
Not Exported
As far as is known, all RNA transcripts of
mtDNA and their translation products remain
in the mitochondrion, and all mtDNA-encoded
proteins are synthesized on mitochondrial
ribosomes. Mitochondria encode the rRNAs
that form mitochondrial ribosomes, although
all but one or two of the ribosomal proteins (depending on the species) are imported from
the cytosol.
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Products of Mitochondrial Genes Are
Not Exported
Reflecting the bacterial ancestry of mitochondria, mitochondrial ribosomes resemble bacterialribosomes and differ from cytoplasmic ribosomesin their RNA and protein composition .
chloramphenicol blocks protein synthesis bybacterial and most mitochondrial ribosomes, butnot by cytoplasmic ribosomes. Conversely, cycloheximide inhibits protein synthesis by
eukaryotic cytoplasmic ribosomes but does notaffect protein synthesis by mitochondrialribosomes or bacterial ribosomes.
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Mitochondrial Genetic Codes Differ
from the Standard Nuclear Code
The genetic code used in animal and fungal
mitochondria is different from the standard
code used in all prokaryotic and eukaryotic
nuclear genes; remarkably, the code even
differs in mitochondria from different species
Why and how this phenomenon happened
during evolution is mysterious.
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Mitochondrial Genetic Codes Differ
from the Standard Nuclear Code
UGA, for example, is normally a stop codon,
but is read as tryptophan by human and
fungal mitochondrial translation systems;
however, in plant mitochondria, UGA is still a
stop codon. AGA and AGG, the standard
nuclear codons for arginine also code for
arginine in fungal and plant mtDNA, but theyare stop codons in mammalian mtDNA and
serine codons in Drosophila mtDNA.
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DNA IN CHLOROPLASTS
In contrast to other eukaryotes, which contain asingle type of mtDNA, plants contain severaltypes of mtDNA that appear to recombine witheach other. Plant mtDNAs are much larger andmore variable in size than the mtDNAs of otherorganisms.. The mitochondrial rRNAs of plants are also considerably larger than those of othereukaryotes. The recent sequencing of one of the
smallest plant mtDNAs has revealed that long, noncoding regions and duplicated sequences arelargely responsible for the greater length of plantmtDNAs.
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DNA IN CHLOROPLASTS
Differences in the size and coding capacity of mtDNA from various organisms most likely reflectthe movement of DNA between mitochondria
and the nucleus during evolution. Direct evidencefor this movement comes from the observationthat several proteins encoded by mtDNA in somespecies are encoded by nuclear DNA in others. It
thus appears that entire genes moved from themitochondrion to the nucleus, or vice versa, during evolution.
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Chloroplasts Contain Large Circular DNAs
Encoding More Than a Hundred Proteins
The structure of chloroplasts is similar in many
respects to that of mitochondria. Like mitochondria,
chloroplasts contain multiple copies of the organellar
DNA and ribosomes, which synthesize somechloroplast-encoded proteins using the standard
genetic code. Other chloroplast proteins are
fabricated on cytosolic ribosomes and are
incorporated into the organelle after translation. Chloroplast DNAs are circular molecules of 120,000
160,000 bp, depending on the species.
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Chloroplasts Contain Large Circular
DNAs Encoding More Than a Hundred
Proteins Of the 120 genes in chloroplast DNA, about 60 are
involved in RNA transcription and translation, includinggenes for rRNAs, tRNAs, RNA polymerase subunits, andribosomal proteins. About 20 genes encode subunits of the chloroplast photosynthetic electron transportcomplexes and the F0F1 ATPase complex. Also encodedin the chloroplast genome is the larger of the twosubunits of ribulose 1,5-bisphosphate carboxylase,
which is involved in the fixation of carbon dioxideduring photosynthesis.
.
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Chloroplasts Contain Large Circular
DNAs Encoding More Than a Hundred
Proteins Reflecting the endosymbiotic origin of
chloroplasts, some regions of chloroplast DNA arestrikingly similar to those of the DNA of present-
day bacteria. For instance, chloroplast DNAencodes four subunits of RNA polymerase thatare highly homologous to the subunits of E. coli
RNA polymerase. One segment of chloroplast
DNA encodes eight proteins that are homologous to eight E. coli ribosomal proteins; the order of these genes is the same in the two DNAs
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MITOCHONDRIA-SUMMARY
Mitochondria and chloroplasts are believedto have evolved from bacteria that formed asymbiotic relationship with ancestral cells
containing a eukaryotic nucleus. Most of thegenes originally within these organelles havebeen transferred to the nuclear genome overevolutionary time, leaving different genes inthe organelle DNAs of different organisms.
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MITOCHONDRIA-SUMMARY
mtDNAs are only 16 kb in length; they contain
no introns and very little noncoding DNA. Yeast
and plant mtDNAs are much longer. All mtDNAs
encode rRNAs, tRNAs, and some of the proteins involved in mitochondrial electron transport and
A TP synthesis.
Most mtDNA is inherited from egg cells ratherthan sperm, and mutations in mtDNA result in a
maternal cytoplasmic pattern of inheritance.
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MITOCHONDRIA-SUMMARY
Mitochondrial ribosomes resemble bacterialribosomes in their structure, sensitivity tochloramphenicol, and resistance to cycloheximide.
The genetic code of animal and fungal mtDNAs differs from that of bacteria and the nuclear genomein that several codons encode alternative aminoacids or stop signals. The mitochondrial code differs
between different animals and fungi. Plantmitochondria appear to use the standard nuclearand bacterial genetic code.
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MITOCHONDRIA-SUMMARY
Mutations in mtDNA can cause human
neuromuscular disorders, probably because of
the high demand for ATP in these tissues.
Patients generally have a mixture of wild-type
and mutant mtDNA in their cells
(heteroplasmy). The severity of the phenotype
is greater, the higher the fraction of mutantmtDNA.
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PROKARYOTIC GENOMES
Single short circular chromosome present.
None or few structural proteins present.
Genomes augmented by plasmids DNA.
The chromosome has a single set of genes hence haploid save for those encoding for therRNA.
90% of the DNA encodes polypeptides orstable RNA,10% is used for controlling geneexpression or has a purely structural function.
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PROKARYOTIC GENOMES
Have less junk DNA 10-15%(i.e.non coding
DNA that is probably largely remnants of
genes that have been lost during the course of
evolution).
Genome sizes range from 0.6-over 10mb pairs.
Domains of circular genome tend to be
pinched off the loop of supercoiled DNA to
form small supercoiled domains.
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PROKARYOTIC GENOMES
Because the genomes are relatively small and
contained in one circular molecule,only one
replication initiation site known as the ori is
needed.This accounts for the quick division
rates in prokaryotes because the ori sequence
is regenerated first during replication
providing a new site for replication to begineven as the original round of replication is still
proceeding.
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PROKARYOTIC GENOMES
Since prokaryotic chromosomes have no ends, the entire genome can be copied.
There are no telomeres in prokaryotic genomes.
Prokaryotic DNA is substantially less packedduring cell division than in eukaryotes.This is because:-
1. The genome is small.
2. There is no nuclear membrane.
3. The DNA is circular (has no loose ends).
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PROKARYOTIC GENOMES.
In a prokaryotic genome, there is generally
only one copy of each gene, and thus the
dominant/recessive phenomenon does not
apply.
Each and every gene will be expressed,
making prokaryotes a much
better vehicle for developing new genes.
There is no interference from dominant
forms.
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PROKARYOYIC GENOMES.
Disadvantageous forms of a gene are much less
likely to persist in a community of prokaryotes,
since a more advantageous dominant form of the
gene cannot cover for it.
This is but one reason why prokaryotes tend to
have much greater rates of change in their genomes than eukaryotes.
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