GENOMES IN PROKARYOTES AND

EUKARYOTES.
DR KITYAMUWESI RICHARD
MDENT(ORAL AND MAXILLO-FACIAL
SURGERY)
GENOMES
• Genome is the total genetic information of an
organism.
• For most organisms, it is the complete DNA
sequence.
• For RNA viruses, the genome is the complete
RNA sequence, since their genetic information
is encoded in RNA.
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 (for single-
stranded DNA or RNA).
GENOMES IN EUKARYOTIC CELLS.

•Nuclear DNA
•Mitochondrial DNA
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.
DNA STRUCTURE
• A DNA molecule has two strands that are
intertwined with each other to form a "double
helix" structure, also known as the B form, the
helix makes a turn every 3.4 nm, and the distance
between two neighboring base pairs is 0.34 nm. 
Hence, there are about 10 pairs per turn.  The
intertwined strands make two grooves of different
widths, referred to as the major groove and the
minor groove, which may facilitate binding with
specific proteins.
DNA STRUCTURE
• In a solution with higher salt
concentrations or with alcohol
added, the DNA structure may
change 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.
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 in
alcohol 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.
THE NORMAL RIGHT-HANDED "DOUBLE HELIX"
STRUCTURE OF DNA, ALSO KNOWN AS THE B FORM.
CHROMATIN
•Chromatin is the substance which becomes visible
chromosomes during prophase of cell division.  Its
basic unit is nucleosome, composed of 146 bp
DNA and eight histone proteins.  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.
CHROMATIN
• The 30 nm chromatin fiber is associated with
scaffold proteins (notably topoisomerase II) to form
loops.  Each loop contains about 75 kb DNA.  Scaffold
proteins are attached to DNA at specific regions
called scaffold attachment regions (SARs), which are
rich 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 nucleotide
pairs while R bands are rich in G-C nucleotide pairs.
STRUCTURE OF CHROMATIN
STRUCTURE OF NUCLEOSOMES
•Histones are the proteins closely responsible
for the structure of chromatin and play
important roles in the regulation of gene
expression. Five types of histones have been
identified: H1 (or H5), H2A, H2B, H3 and H4.
• H1 and its homologous protein H5 are Linker
histones they stabilize the solenoid structure
of chromatin.
 STRUCTURE OF NUCLEOSOMES
•The other four types of histones associate with
DNA 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, H3 and
H4.  The DNA is wrapped around the histone core,
making nearly two turns per nucleosome.
 
3-D STRUCTURE OF A NUCLEOSOME
GENERAL ORGANISATION OF DNA SEQUENCE
DNA STRUCTURE
• A typical DNA molecule consists of genes,
pseudogenes and extragenic region.
• Pseudogenes are nonfunctional genes.  They often
originate from mutation of duplicated genes .
• 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 or RNA. 
The coding region accounts for about 3% of the total
DNA in a human cell.
GENES
• A gene is a unit of genetic information that
provides instruction for a particular property of
an organism.
• It includes the entire nucleotide sequence
necessary for the expression of its product
(peptide or RNA).
• Each gene may exist in alternative forms called
alleles.
• A gene is the fundamental unit of heredity. 
GENE STRUCTURE.
GENE STRUCTURE.
• A gene sequence may be divided into regulatory
and transcriptional regions.
•   The regulatory region could be near or far from
the transcriptional region. 
• The transcriptional region consists of exons and
introns. 
• Exons encode a peptide or functional RNA. 
• Introns will be removed after transcription by
splicesomes and self-splicing.
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.
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.
HUMAN MITOCHONDRIAL DNA
(eukaryotic cell)

• There is no effective DNA

repair system in the
mitochondria hence mutations
occur.
• Is maternal in origin.
Mitochondria Contain Multiple mtDNA
Molecules
• Individual mitochondria are large enough
to be seen under the light microscope
and even the mitochondrial DNA
(mtDNA) can be detected by
fluorescence microscopy. The mtDNA is
located in the interior of the
mitochondrion, the region known as the
matrix.
Mitochondria Contain Multiple mtDNA
Molecules
• All the mitochondria in eukaryotic
cells contain multiple mtDNA
molecules. Thus the total amount of
mtDNA in a cell depends on the
number of mitochondria, the size of
the mtDNA, and the number of
mtDNA molecules per mitochondrion
MITOCHONDRIAL GENES

• Have a cytoplasmic
inheritence.
• mtDNAs encode rRNAs, tRNAs,
and essential mitochondrial
proteins.
MITOCHONDRIAL GENES
• All proteins encoded by mtDNA are synthesized on
mitochondrial ribosomes. All mitochondrially
synthesized polypeptides identified thus far (with
one possible exception) are not complete enzymes
but subunits of multimeric complexes used in
electron transport or ATP synthesis. Most proteins
localized in mitochondria, such as the mitochondrial
RNA and DNA polymerases, are synthesized on
cytoplasmic ribosomes and are imported into the
organelle .
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.
Products of Mitochondrial Genes Are Not
Exported
• Reflecting the bacterial ancestry of mitochondria,
mitochondrial ribosomes resemble bacterial
ribosomes and differ from cytoplasmic ribosomes in
their RNA and protein composition .
• chloramphenicol blocks protein synthesis by bacterial
and most mitochondrial ribosomes, but not by
cytoplasmic ribosomes. Conversely, cycloheximide
inhibits protein synthesis by eukaryotic cytoplasmic
ribosomes but does not affect protein synthesis by
mitochondrial ribosomes or bacterial ribosomes.
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.
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 they
are stop codons in mammalian mtDNA and
serine codons in Drosophila mtDNA.
DNA IN CHLOROPLASTS

• In contrast to other eukaryotes, which contain a single

type of mtDNA, plants contain several types of mtDNA
that appear to recombine with each other. Plant
mtDNAs are much larger and more variable in size than
the mtDNAs of other organisms.. The mitochondrial
rRNAs of plants are also considerably larger than those
of other eukaryotes. The recent sequencing of one of
the smallest plant mtDNAs has revealed that long,
noncoding regions and duplicated sequences are largely
responsible for the greater length of plant mtDNAs.
DNA IN CHLOROPLASTS
• Differences in the size and coding capacity of
mtDNA from various organisms most likely reflect
the movement of DNA between mitochondria and
the nucleus during evolution. Direct evidence for
this movement comes from the observation that
several proteins encoded by mtDNA in some species
are encoded by nuclear DNA in others. It thus
appears that entire genes moved from the
mitochondrion to the nucleus, or vice versa, during
evolution.
 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 some
chloroplast-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.
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, including
genes for rRNAs, tRNAs, RNA polymerase subunits, and
ribosomal proteins. About 20 genes encode subunits of
the chloroplast photosynthetic electron transport
complexes and the F0F1 ATPase complex. Also encoded in
the chloroplast genome is the larger of the two subunits
of ribulose 1,5-bisphosphate carboxylase, which is
involved in the fixation of carbon dioxide during
photosynthesis.
• .
Chloroplasts Contain Large Circular DNAs
Encoding More Than a Hundred Proteins
• Reflecting the endosymbiotic origin of chloroplasts,
some regions of chloroplast DNA are strikingly
similar to those of the DNA of present-day bacteria.
For instance, chloroplast DNA encodes four
subunits of RNA polymerase that are 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
MITOCHONDRIA-SUMMARY
• Mitochondria and chloroplasts are believed to have
evolved from bacteria that formed a symbiotic
relationship with ancestral cells containing a
eukaryotic nucleus. Most of the genes originally within
these organelles have been transferred to the nuclear
genome over evolutionary time, leaving different
genes in the organelle DNAs of different organisms.
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 rather
than sperm, and mutations in mtDNA result in
a maternal cytoplasmic pattern of inheritance.
MITOCHONDRIA-SUMMARY
•Mitochondrial ribosomes resemble bacterial ribosomes in
their structure, sensitivity to chloramphenicol, and resistance
to cycloheximide.

• The genetic code of animal and fungal mtDNAs differs from

that of bacteria and the nuclear genome in that several codons
encode alternative amino acids or stop signals. The
mitochondrial code differs between different animals and
fungi. Plant mitochondria appear to use the standard nuclear
and bacterial genetic code.
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 mutant
mtDNA.
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 the rRNA.
• 90% of the DNA encodes polypeptides or stable
RNA,10% is used for controlling gene expression
or has a purely structural function.
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.
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 begin
even as the original round of replication is still
proceeding.
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 packed during
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).
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.
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.