Principal differences between prokaryotic and eukaryotic cells

STBP1013 Fundamentals of Molecular Biology

Gene Organization and Structure in

Eukaryote and Prokaryote

Prokaryote vs eukaryote Prokaryote

• Defines as a single-celled organism that lacks a
Prokaryotes Eukaryotes membrane-bound nucleus (karyon), mitochondria, or
any other membrane-bound organelle
Single cell Single or multi cell
• The word prokaryote comes from the Greek πρό- (pro-)
No nucleus Nucleus "before" and καρυόν (karyon) "nut or kernel"
• All the intracellular water-soluble components
One piece of circular DNA Chromosomes (proteins, DNA and metabolites) are located together in
the same volume enclosed by the cell membrane,
No mRNA post-transcriptional rather than in separate cellular compartments
Exons/Introns splicing
modification • Prokaryotes, however, do possess protein-based
microcompartments, which are thought to act as
primitive organelles (protein-bounded and lipid-bounded
organelles)
– some prokaryotes also have multicellular stages in
their life cycles, such as myxobacteria, or create
large colonies, like cyanobacteria

Prokaryote Prokaryote vs eukaryote

• The organization of prokaryotic DNA therefore differs
from that of eukaryotes in several important ways
• The most notable difference is the condensation
process that prokaryotic DNA molecules undergo in
order to fit inside relatively small cells
• Prokaryotic cells can be divided into two domains,
Archaea and Bacteria
– distinctive types of prokaryotes include
extremophiles and methanogens; these are
common in some extreme environments
• Molecular studies have provided insight into the
evolution and interrelationships of the three domains
of biological species
• Eukaryotes is the third domain
– it includes humans, whose cells have a well-defined
membrane bound nucleus (containing chromosomal
DNA) and organelles
• The division between prokaryotes and eukaryotes
reflects the existence of two discrete levels of cellular
organization

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 Prokaryote vs eukaryote
• The division between prokaryotes and eukaryotes is
usually considered the most important distinction or
difference among organisms
• The distinction is that eukaryotic cells have a "true"
nucleus containing their DNA, whereas prokaryotic
cells do not have a nucleus
• Both eukaryotes and prokaryotes contain large
RNA/protein structures called ribosomes, which
produce protein
Prokaryote
• The genome in a prokaryote is held within a
DNA/protein complex in the cytosol called the nucleoid,
which lacks a nuclear envelope
• The complex contains a single, cyclic, double-
stranded molecule of stable chromosomal DNA, in
contrast to the multiple linear, compact, highly
organized chromosomes found in eukaryotic cells
• In addition, many important genes of prokaryotes are
stored in separate circular DNA structures called
plasmids
Prokaryote
• Prokaryotic cells are usually much smaller than
eukaryotic cells
• Therefore, prokaryotes have a larger surface-area-to-
volume ratio, giving them a higher metabolic rate, a
higher growth rate, and as a consequence, a shorter
generation time than eukaryotes
Prokaryote vs eukaryote
• Another difference is that ribosomes in prokaryotes are
smaller than in eukaryotes
• However, two organelles found in many eukaryotic cells,
mitochondria and chloroplasts, contain ribosomes
similar in size and makeup to those found in
prokaryotes
• This is one of many pieces of evidence that
mitochondria and chloroplasts are themselves
descended from free-living bacteria
• This theory holds that early eukaryotic cells took in
primitive prokaryotic cells by phagocytosis and
adapted themselves to incorporate their structures,
leading to the mitochondria we see today
Prokaryote
• Prokaryotes lack mitochondria and chloroplasts
– processes such as oxidative phosphorylation and
photosynthesis take place across the prokaryotic
cell membrane
• However, prokaryotes do possess some internal
structures, such as prokaryotic cytoskeletons
• It has been suggested that the bacterial order
Planctomycetes (aquatic bacteria) have a membrane
around their nucleoid and contain other membrane-
bound cellular structures
• However, further investigation revealed that
Planctomycetes cells are not compartmentalized or
nucleated and like the other bacterial membrane
systems are all interconnected
Size of prokaryotes
• Most prokaryotes are between 1 µm and 10 µm, but
they can vary in size from 0.2 µm to 750 µm
• The sizes of prokaryotes relative to other organisms and
biomolecules are as below:
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 Eukaryote
• A eukaryote is any organism whose cells contain a
nucleus and other structures (organelles) enclosed
within membranes
• Eukaryotes are formally the taxon Eukarya or
Eukaryota
• The defining membrane-bound structure that sets
eukaryotic cells apart from prokaryotic cells is the
nucleus, enclosed by the nuclear envelope, which
contains the genetic material
• The presence of a nucleus gives eukaryotes their name,
which comes from the Greek ευ (eu) "well" and κάρυον
(karyon) "nut or kernel"
Cell division in eukaryotes
• Cell division in eukaryotes is different from that in
organisms without a nucleus (prokaryotes)
• There are two types of division processes
– in mitosis, one cell divides to produce two
genetically identical cells
– in meiosis, which is required in sexual
reproduction, one diploid cell (having two instances
of each chromosome, one from each parent)
undergoes recombination of each pair of parental
chromosomes, and then two stages of cell
division, resulting in four haploid cells (gametes),
with each gamete has just one complement of
chromosomes, and each a unique mix of the
corresponding pair of parental chromosomes
Prokaryotic genes
• Perhaps due to the space constraints of packing so
many essential genes onto a single chromosome,
prokaryotes can be highly efficient in terms of
genomic organization i.e. very little space is left
between prokaryotic genes
• As a result, noncoding sequences account for an
average of 12% of the prokaryotic genome, as opposed
to upwards of 98% of the genetic material in
eukaryotes
Eukaryote
• Most eukaryotic cells also contain other membrane-
bound organelles such as mitochondria or the Golgi
apparatus
• In addition, plants and algae contain chloroplasts
• Many unicellular organisms are eukaryotes, such as
protozoa
• All multicellular organisms are eukaryotes, including
animals, plants and fungi
Eukaryotic cell
• Eukaryotic cells are typically much larger than those
of prokaryotes
• They have a variety of internal membranes and
structures, called organelles, and a cytoskeleton
composed of microtubules, microfilaments and
intermediate filaments, which play an important role in
defining the cell's organization and shape
• Eukaryotic DNA is divided into several linear bundles
called chromosomes, which are separated by a
microtubular spindle during nuclear division
Prokaryotic genes
• Furthermore, unlike eukaryotic chromosomes, most
prokaryotic genomes are organized into polycistronic
operons, or clusters of more than one coding region
attached to a single promoter, separated by only a few
base pairs
• The proteins encoded by each operon often
collaborate on a single task, such as the metabolism
of a sugar into by-products that can be used for energy
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 Operon The prokaryotic lac operon
• A functioning unit of genomic DNA containing a
cluster of genes under the control of a single
promoter
• Originally, operons were thought to exist solely in
prokaryotes, but since the discovery of the first
operons in eukaryotes in the early 1990s, more
evidence has arisen to suggest they are more common
than previously assumed
• In general, expression of prokaryotic operons leads to
the generation of polycistronic mRNAs, while • Three structural genes code for proteins involved in lactose import
eukaryotic operons lead to monocistronic mRNAs and metabolism in bacteria
• The genes are organized together in a cluster called the lac operon
• The lac operon in bacteria includes a promoter, an operator and three
structural genes
• These regions occur in a specific arrangement

The prokaryotic lac operon Eukaryotic genes

• In the diagram, the operon is presented in order from left to right The major structures in DNA compaction
• The following regions are shown: first the promoter in red, then the DNA, the nucleosome, the 10nm "beads-on-a-string" fibre, the 30nm fibre,
operator in yellow, and finally the three structural genes, which the active chromosome and the metaphase chromosome
include beta-galactosidase in blue, beta-galactoside permease in
dark pink, and beta-galactoside transacetylase in orange
• Additional regulatory sequences are located to the left of the promoter
in the region, upstream of the lac operon

Eukaryotic genes Eukaryotic genes

• Genes are the basic physical and • A locus describes the region of a
functional units of heredity chromosome where a gene is located
• Each gene is located on a • 11p15.5 is the locus for the human
particular region (locus) of a insulin gene
chromosome and has a specific • 11 is the chromosome number, p
ordered sequence of nucleotides indicates the short arm of the
chromosome, and 15.5 is the number
assigned to a particular region on a
chromosome
• When chromosomes are stained in
the lab, light and dark bands
appear, and each band is
numbered
• The higher the number, the farther
away the band is from the
centromere

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 Eukaryotic gene organization
• In the late 1970s, it was discovered that the open
reading frames for genes of multicellular organisms are
typically interrupted by regions of noncoding DNA
sequence called introns
• This means that when the gene is transcribed, the
primary transcript spans more genomic terrain than
would be indicated by the length of the coding sequence
• Introns are initially transcribed but then removed
from the mature messenger RNA (mRNA) by a process
called splicing
• The sequence that remains in the mRNA consists of
what are called exons
Gene splicing
DNA 1 2 3 but excised prior to translation
Pre-mRNA 1 2 3
Spliced mRNA 1 2 3 required for translation of the mature mRNA into a
• Exons are sequences of DNA that are expressed into protein
• Introns are intervening sequences that are not translated into protein
Splice-site consensus sequences
• Most of the recognition sequences for splice donors and acceptors lie
in the introns
• Capital letters indicate a base that is found consistently in that
position, small letters indicate bases that are found typically
• Pyrimidine tracts (yyy) lie in the intron near the acceptor site
• The letter ‘n’ indicates that any one of the four nucleotides are found
in this position
Eukaryotic gene structure
• Most of the genes consist of short coding sequences or
exons that are interrupted by a longer intervening
noncoding sequence or introns; although a few genes
in the human genome have no introns
Gene splicing
• An intron is a portion of the gene that is transcribed
• An exon is a portion of the gene that appears in both
the primary and the mature mRNA transcripts
• When spliced correctly, exons reconstruct the open
reading frame that contains the coding information
functional polypeptide
• Analysis of thousands of intron-exon boundaries has
shown that there are consensus sequences for
splice-site recognition
Gene splicing
• After transcription, introns are removed by the cellular splicing
machinery
• Alternative usage of exons allows the inclusion or exclusion of
amino acid domains in the polypeptide sequence
• Shown above is an alternatively splice transcript comprising a truncated
form of exon 6 and the deletion of exon 8
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 Gene splicing Gene splicing
• The differences in the polypeptide sequences
translated from these mRNAs often result in proteins
with diverse functions
• For example, alternative splicing can result in both
membrane-bound and secreted forms of receptors
or can alter the binding properties of receptors,
depending on which exons are present in the mature
transcript
• In some cases (e.g. a family of genes expressed in
brain called ‘neurexins’) up to thousands of different
• The bundling of coding sequences into exons increases the isoforms (i.e. splice forms) can be potentially generated
complexity of the coding capacity of a genome owing to a process from the same primary transcript
called alternative splicing
• Different mature mRNAs can be produced from a primary transcript
by leaving out one or more exons or by using different splice sites
in an exon

Prokaryotic vs Eukaryotic Genomes

Eukaryotic gene structure
Characteristics Prokaryotes Eukaryotes

Size of genome 104 to 107 106 to 1011

Repetitive sequences Small amount Large amount

Segments of non-coding Rare Usual

DNA within coding
sequence
DNA segregated within No Yes
nucleus
Number of chromosomes Few (often only one) Many
in genome
Organization of genes Often polycistronic* Usually monocistronic*

Polycistronic is the term used to describe a messenger RNA molecule that contain
the genetic information to translate more than one polypeptide or protein. Most of
the messenger RNA molecules found in prokaryotes are polycistronic.
Messenger RNA molecules that encode a single polypeptide are termed
monocistronic and occur mainly in eukaryotes.

Prokaryotic vs Eukaryotic Chromosomes Prokaryotic vs Eukaryotic Genes

Prokaryotic chromosomes
• Many prokaryotes contain a single
circular chromosome
• Prokaryotic chromosomes are
condensed in the nucleoid via DNA
supercoiling and the binding of
various architectural proteins
• Because prokaryotic DNA can
interact with the cytoplasm,
transcription and translation occur
simultaneously
• Most prokaryotes contain only one
copy of each gene (i.e. they are
haploid)
• Nonessential prokaryotic genes are
commonly encoded on
extrachromosomal plasmids
• Prokaryotic genomes are efficient
and compact, containing little
repetitive DNA
Eukaryotic chromosomes
• Eukaryotes contain multiple linear Prokaryotes Eukaryotes
chromosomes
• Eukaryotic chromosomes are • Prokaryotes have fewer genes • Eukaryotes generally have many
condensed in a membrane-bound and these genes are all located more genes and these genes
nucleus via histones on one chromosome are spread across multiple
chromosomes
• In eukaryotes, transcription occurs
• Groups of genes producing • Eukaryotes have mRNA that
in the nucleus, and translation
proteins with related functions must have its introns excised
occurs in the cytoplasm
are often organized into operons and the mRNA transported out
• Most eukaryotes contain two copies of the nucleus to the ribosomes
of each gene (i.e. they are diploid)
• Extrachromosomal plasmids are
not commonly present in eukaryotes
• Eukaryotes contain large amount of
noncoding and repetitive DNA

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 Gene families
• A gene family is a set of several similar genes,
formed by duplication of a single original gene, and
generally with similar biochemical functions
– e.g. genes for human haemoglobin subunits (the
ten genes are in two clusters on different
chromosomes, called the α-globin and β-globin
loci)
• Genes are categorized into families based on shared
nucleotide or protein sequences
• Phylogenetic techniques can be used as a more
rigorous test
Gene families
• The positions of exons within the coding sequence
can be used to infer common ancestry
• Knowing the sequence of the protein encoded by a
gene can allow researchers to apply methods that find
similarities among protein sequences that provide
more information than similarities or differences among
DNA sequences
• Furthermore, knowledge of the protein's secondary
structure gives further information about ancestry,
since the organization of secondary structural
elements presumably would be conserved even if the
amino acid sequence changes considerably
• These methods often rely upon predictions based
upon the DNA sequence

Gene families
• If the genes of a gene family encode proteins, the term
protein family is often used in an analogous manner to
gene family
• The expansion or contraction of gene families along a
specific lineage can be due to chance, or can be the
result of natural selection
• To distinguish between these two cases is often
difficult in practice
• Recent work uses a combination of statistical models
and algorithmic techniques to detect gene families
that are under the effect of natural selection