Lecture schedule 3

prokaryotes and eukaryotes

Bacterial classification
The 5 kingdom system of classification places all prokaryotes in the kingdom
Monera and eukaryotes in protista
Fig. *******
Five kingdom classification
Kingdom
1. Monera

Characteristics
Prokaryotic
-

unicellular

lack of true nuclei and cell organelles

DNA has little or no protein Nutrition by

absorption or by photosynthesis or chemo
synthesis

2. Protista

Reproduction asexual binary fission

Eukaryotic
-

Unicellular

True

membrane

bound

nucleus

and

organelles within their cytoplasm

-

Nutrition by ingestion or photosynthesis

or absorption

3. Fungi

Reproduction Asexual and sexual.

Eukaryotic
-

Uni or multicellular

Nutrition by absorption

Reproduction Asexual and sexual.

Life cycle - complex

4. Plantae

5. Animalia

Eukaryotic
-

Multicellular

Nutrition by photosynthesis

Eukaryotic
-

Multicellular

Nutrition by ingestion or absorption

Reproduction primarily sexual.

Later in 1970s Woese and co workers reclassified all living things into 3 primary
kingdoms viz., eukaryotes, eubacteria and archaebacteria based on partial sequence
homology of 16s rRNA of many diverse prokaryotes and the corresponding small subunit
of rRNA of eukaryotes.
In 1977 T. Cavalier Smith of Kings college, London, proposed that archaebacteria
arose from a group of gram +ve bacteria similar to present day actinomycetes which were
once thought to be fungi.
In 1988, A.Lake of Univ. California proposed the following model. One branch
gave ride the eubacteria and 2 groups of archaebacteria (extreme salt halophilic and
methanogenic) and another branch to the eukaryotes and acidophilic archaebacteria called
eocytes (grow well in hot acidic environments)

Comparison of archaebacteria, eubacteria and eukaryotes

Characters

Archaebacteria

Eubacteria

Eukaryotes

1. Cell wall

Lack peptide

Contain peptido

Absent or

glycan

glycan

made of other
materials

2. Lipids of cell membrane

3. Protein synthesis

Branched chain

Straight chain

Straight chain

fattyacids

fatty acids

FA and sterols

Not impaired by

Impaired by

Mostly not

antibiotics such as

chlorempheniol

impaired by

chlorempheniol

antibiotics.

4. First amino acid in a Methionine

Formyl

Methionine

protein
5. Habitat

Extreme

methionine
Wide range of

Wide range of

environments

environments

environments

Similarities and differences between prokaryotic and eukaryotic cells

Characters
1. Organisms

Prokaryotes
Primitive

Eukaryotes
Protozoa,algae and

archaebacteria,

fungi

photosynthetic
cyanobacteria
2. Genetic information

3. Location of Genetic information

Found in single

In paired

chromosome

chromosome

Nuclear area

Membrane bound

(Nucleoid)

nucleus

(region where the

genome present)

4. Nucleolus (site of rRNA synthesis)

Absent

Present

5. Histones

Absent

Present

6. Extra chromosal DNA

In plasmids

In mitochondria,

7. Mitotic spindle

Absent

chloroplasts
Present during cell

8. Plasma membrane

Fluid mosaic

division
FMS contains

structure lacks

sterols

sterols
9. Internal membrane

Only in

Numerous

photosynthetic

membrane bound

organisms

organelles.

10. Endoplasmic reticulum

Absent

Present

11. Respiratory enzymes

Cell membrane

Mitochondria

12. Chromatophores

Present in

Absent

photosynthetic
bacteria
13. Chloroplasts
14. Golgi apparatus

Absent
Absent

Present in some
Present

15. Lyso somes

Absent

Present

16. Peroxisomes

Absent

Present

17. Ribosomes

70s

80s in cytoplasm
and in endoplasmic
reticulum; 70s in

organelles
18. Cytoskeleton

Absent

Present

19. Cell wall

Usually

Cellulose, chitin or

peptidoglycon found both found on plant

20. External wall

21. Flagella

in most cells

and fungal cells

Capsule or slime

Pellicle, shell in

player

some cases

Consists of fibrils or

Complex membrane

flagell in when

bound structure with

present

9+2 micro tubule

arrangement when it
is present

22. Cilia

Absent

Present shorter than

but similar to
flagella in some
eukaryotic cells.

23. Pili

Present as

Absent

attachment or
conjugation pili in
some prokaryotic
cells
24. Size

25. Sexuality

1-2 by 1-4m or

>5m in width or

less

dia

Zygote is mero

Zygote is diploid.

zygotic (partially

diploid)
26. DNA base ratio as mole % G+ C (G+C 28-73

About 40

%)

Genetic elements in prokaryotes

The genetic elements such as chromosome, plasmid, transposons and insertion
sequences are common both for prokaryotes and eukaryotes. But the genetic elements
viz., mitochondria and chloroplasts are present only in respiratory and photosynthetic
eukaryotes.
Chromosome of prokaryotes
Though eubacteria and archaebacteria are prokaryotes, they have completely
different chromosome structure.
Eubacterial chromosomes
1.

The chromosome is single and circular mostly but sometimes linear as in Borelia sp,
streptomyces sp.etc.

2.

Largest in size (>1mm) and many fold larger than the length of the cell.

3.

The mol. wt of E.coli chromosome is 2.56 x 109 and the size is 3.8 x 10 3 kbp. Many
bacteria have similar size. Usually the size of the chromosome correlates with the
physiological or morphological complexity. More complex the metabolic activity
more will be the size of the chromosome.
Genetic Elements (GE)
GE. Common to Pro & Eukaryotes

Genome total complement of genes in a cell or virus.

GE. Structure containing genetic material.

Chromosomal

chromosomes

GE
Non chromosomal

Plasmids
Transposans
Mitochondria
Chloroplasts
Viruses

Excl. Eukaryotes Mitochondria (Respiratory) and chloroplasts (Photosynthetic)

Viral genome single or ds DNA or RNA molecules for both cases
Viruses genome (DNA or RNA) control virus rep transfer from cell to cell viral
genome to-chromosomes contains genes essential to virus and not to host cell.
Functionally distinct from cellular chromosome.
- Both Linear and circular shape of chromosome
- Some cases, integrated with cellular chromosomes.
Eubacterial chromosome
-

Mostly single and circular (ex. Borelia burgdorfere, Linear) (cause lyme
disease) Streptomyces coelicolor
Two in Rhodobacter sphaeroides;
3-Halobacter sp NRC -1
Size largest (>1mm)
Always correlation between size and physiological or morphological complexity,
more size more complexity.

E.coli
Desulfovibrio
Mycoplasma
Myxococcus xanthin
Anabaena
Calothrix

Mol. Wt.
2.56 x 109
1.1 x 109
0.4 x 109
3.79 x 109
3.17 x 109
8.58 x 109

Size
3.8 x 103 kbp
< size of E.coli
< 5-6 times E.coli
> time E.coli
> time E.coli
> 3 times E.coli

Mol. Wt Gene number and genome protein

M.wt bac. Protein 45,000 (Average)
- Absence of nuclear membrane and nucleolus
- Simultaneous transcription and translation.
Archaebacterial chromosome
- DNA condensation by wrapping round a proteinaceous core.
- Presence of DNA proteins (HTa) 4 nos.
- Presence of nucleosome like complexes.

Thermoplasma has histone like protein similar to HTa.

Sizes, shapes and numbers of chromosomes in selected prokaryotes

Mycoplasma
genitallium
Borelia burgdorferi
(17 circular Linear
plasmids 0.5mb)
H.influenzae
(First cellular organism
genome sequenced)
Rhodobacter
sphaeroides
(Chr.1 3.1 mb;
Chr. 2 0.9 mb)
B. subtilis
E.coli K-12
Streptomyces coelicolor
Archaea
Methanococus
jonnashii
Pyrococcus abyssi
Halobacterium sp
NRCI
(C large chr. 1-2.01 MB
Minichr 2-0.19MB,
0.37MB)
Sulfolobus solfatarius

Size(Mb)
0.58

No
1

Shape
O (C)

0.91

(L)

1.83

(C)

G-ve, phototrophic

4.00

(C)

G+ve, genetic model

G-ve, genetic model
Actinomycete,
antibiotic producer

4.21
4.64
8.66

1
1
1

(C)
(C)
(L)

Methanogens grows at
high temp.
High Temp.
High salt

1.66

(C)

1.77
2.57

1
3

(C)
(C)

High temps and High

acidity

2.99

(C)

Smallest known
cellular genome
Lyme disease
(Tick borne disease that
affects humans and
animals. First noticed
in old Lyme,
Connecticut, USA)
G-ve, disease causing

Plasmids
-

Covalently circular, extrachromosomal, ds, self replicating DNA mol. Mostly

circular but some are Linear.
Replicate independently of the host chromosome
Plasmid dif. from virus
i.e- No lysis of host cell
- No extra cellular forms.

F factor plasmid (Tfr F plasmid from F+ to F-)

R factor plasmid (Resistance to antibiotics, heavymetals) and

Bacteriocinogenic plasmid (Lethal protein against closely related spp).

Functions of plasmid
- Pigment production
- Toxin production
- Phage sensitivity and resistance
- Antibiotic production (gene action only under certain conditions)
- Tumor induction
- Host controlled restriction and modification
- Used as genetic vectors.
House keeping genes chromosomes contain genes whose products are involved in
essential metabolic steps under all growth condition. Eg. Gene encoding DNA
gyrase.
Bacterial Genome
-

Primarily an endogenome with 1 or 2 endochromosomes

Components of endogenome may be linear or circular
Bac. chromosomes contain DNA, basic proteins, polyamines and RNA with one
origin of replication
May or may not undergo segment shifting or inversion
Physical and slipped strands mispairing changes occur at noticeable frequency
Plasmids may or may not be present. If present, can exist as free replicon or
integrated as prophages
Has pathogenicity islands
Transposans and Integrans can be inserted in genome.

Transposans
- pieces of DNA- move from one site to another site on a chromosome.
- Jumping genes
- Size <> 10kb Replicate as part of some other molecules of DNA
- IS elements Replication recombination
- Antibiotic and pesticide resistant genes. Reside in central region (core)
Types prokaryotes

IS
Transposons
Special viruses (Mu)

IS elements
- carry no genetic information other than transposition
- size >< 1kb
- Code for own transposition
- Decide the transposing capacity of transposan

Presence of 16-41 bp inverted repeats at the terminal

May present as direct or inverted repeats
Left to right or right to left orientation

Composite transposon
- Carry antibiotic resistance genes
- Flanked by 2 identical copies of IS
- Size 2000 9000 bp
- Transposed between plasmids or phages
Eg Tn5, Tn9, Tn10
Tn3 transposon
- carry 3 genes 1 encode - lactamase other 2 genes code for transposition
- Short inverted repeats of 38bp size.
- Size 5000 bp.
Transposoable phage
- Replicate during transposition
- Transposition as an essential part of their life cycle
Eg. MU, D108 phage.

GE in Eukaryotes
Eukaryotic chromosomes
Chr. No. constant within spp but varies widely among spp.
- Circular or linear; mostly in pairs 80000 100000 bps
- Multiple chromosome even in haploid state.
- Length shorter than lenearized prokaryotic chromosome.
- Contain DNA, Proteins (Histones)
-

Histone Low Mol. wt binding proteins with increased content of basic AA

contribute directly to chromosome (Core histones) structure 5 types 4 present
(H2A, H2B, HS and H4) in 2 copies 1 as single copy.
Chromosomal DNA is packed in Nucleosomes
Nucleosomes (Histones + DNA (165 bp))
Present in every (8 mol-octomers) few hundred bps
No. of introns / gene 0-50.
Presence of introns (non coding seg) and repetitive sequence.
Protein synthesis Transcription and translation spatially separate
Transcription Nucleus; Both exons and introns copied: but introns are removed
when processing of mRNA starts.
Translation cytoplasm after the release of transcribed mRNA
Yeast - 16 chromosomes; only 3 times > than E.coli
Human slightly higher than yeast haploid 200 times more DNA
Linear DNA has Telomere at each end and centromere somewhere between
Telomeres
Centromere important for partitioning the chromosomes during cell division
Telomere Replication of chromosomes they have repetitive DNA a short
sequence (6bps) tandomly repeated from 20 to several hundred times.

Name
Giardia
lamblia
Saccharomyce
s cerevisiae
Dictyostelium
discoideum
Tetrahymena
thermophila

Description
Flagellated
protozoa;
acute
gastroenteritis
Yeast (IST
eukaryotic
genome
sequenced)
Cellular slime
mold
developmental
model
Ciliated
protozoa

Size(MB)
12.00

No
4

Shape
(L)

12.06

16

(L)

3.40

(L)

210.0

(L)

Mitochondria & Chloroplasts

-

site of respiratory enzymes; Major role in energy generation

Non chromosomal
Independently replicating elements but functionally dependant on cellular
chromosomes.
DNA and protein coding system (70s ribosomes, tRNA, translation components,
functional protein)
Most proteins are coded by chromosomal DNA and not by organelle DNA.

Mitochondria
- Power House of the cell
- Carryout TCA cycle & ATP generation by electron transport and oxidative
phosphorylation
- Bounded by 2 membranes with an interspace of 6-8
- Special infoldings of inner membrane CRISTAE
- Ribosomes similar to bacterial ribosomes
- RNA polymerase has core enzymes as that of eubacterial enzymes.
Chloroplasts
- Site of phototrophic ATP formation
- Small, Circular, closed ds DNA
- Bounded by 2 membranes
- Interior compartment STROMA contains DNA, ribosomes, lipid droplets,
starch granules etc Site of dark reaction in CO2 fixation.
- Prominent membrane Thylakoid contains chlorophyll, pigments and electron
carriers site of light reaction in photosynthesis.