MCBL

Cells and Genomes

Prokaryotes and
Eukaryotes
Raj Kandpal, Ph.D.
August 8, 2016
1

Lecture Objectives
After this lecture, students will be able to
describe the:

energy usage in cells

commonality among all living cells
organization of the Tree of Life and its branches
characteristics of prokaryotes including bacterial
anatomy and the significance of the bacterial cell wall and
Gram staining
basic differences between prokaryotic and eukaryotic
cells
importance of genetic variation (mutations) and
mechanisms of genome evolution
key model organisms used in biological research
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Energy Usage

Cells derive energy from

different sources
Organotrophic
Lithotrophic
Phototrophic

Matter & Energy

C, N, H, O, P, S
These elements are abundant in the
nonliving environment (rocks, HOH,
atmosphere)
cant be incorporated into molecules

N2 and CO2 are unreactive

Require free energy to fix them into
organic compounds
5

N and C Fixation
Plants can fix C but not N
Bacteria can fix N (symbiotic
bacteria)
Differences in biochemical
activities have led to
complementation of abilities.
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Tree of Life
Common themes
DNA is a storage of hereditary
information in all living cells
All cells transcribe and translate this
information in similar fashion
All cells use proteins as structure
and also as catalysts
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Diversity of Life
Tree of Life
DNA is a storage of hereditary
information in all living cells
based on genetics, there are three
major groups of organism
Eubacteria
Archaebacteria (Archaea)
Eukarya (Eukaryotes or eucaryotes)
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Tree of Life
Common themes
All living cells have a large free energy
Free energy is required for propagation of
cells (fundamental)
All cells are a biochemical factory (molecular
building blocks are same)
Details of molecular transactions differ

All cells are enclosed in a plasma membrane

Living cells can exist with as few as 500 genes
A core set of over 200 genes is common
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Tree of Life

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Diversity of Life
All living organisms use DNA as their
genetic (hereditary) material
DNA, RNA and proteins have ensured
the success of various species.
DNA sequences have facilitated the
unbiased determination of relatedness
of cells/species
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Comparison of Organisms
Appearance of cells
Microscopic differences
Nucleus or absence of nucleus

Nucleated cells
Eucaryotes

Cells without nucleus

Procaryotes (bacteria)

12

Sequence Based Comparisons

Sequence comparison revealed that:
All bacterial sequences are not similar
Some sequences are closer to eucaryotic cells
than bacterial cells

Procaryotes thus comprise of two

classes:
Eubacteria
Archaebacteria
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Archaea and Eubacteria

Archaea
Found in sewage, ocean depths, salt brines, hot acid
springs (also in less extreme environments)

Phenotypically (appearance) archaea are hard

to distinguish them from eubacteria
At molecular level:
Archaea resemble eucaryotes in machinery for
replication, transcription and translation
Archaea are similar to eubacreia in metabolic
apparatus and energy conversion
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Genes and Evolution

Some parts of genome change more frequently
than other parts
Non-regulatory sequences are free to change
These changes are rate limited only by the frequency of
random errors

Sequences coding for highly optimized essential

proteins cannot alter readily
Such genes are highly conserved and recognizable in all
living species

Conserved genes are important for tracing

evolutionary history of distantly related
organisms
16S rRNA (1500 nt long) was used for classification
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Tree of Life

16
Figure 1-21 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

Bacterial Anatomy

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Diversity of Life
Prokaryotes (procaryotes)
single celled
usually live independently
lack membrane bound organelles
DNA not contained within nucleus
nucleoid
often single-circular chromosome (some have
linear)
Some bacteria have more than one
chromosome
Circular plasmid
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Diversity of Life
Prokaryotes (procaryotes)
many contain a protective cell wall
comprised primarily of peptidoglycan
eubacteria divided into three major types
based on cell wall
Mycoplasma dont have cell wall (some
archaea also lack cell wall)

three major shapes

Rod
Spherical
Spiral
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Common shapes of bacteria

20
Figure 1-17 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

Organization of the Prokaryote

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Figure 1-18a Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

Gram pos. vs. Gram neg cell walls

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Cell Wall: Components

Peptidoglycan
Two sugar derivatives (Nacetylglucosamine, N-acetyl muramic acid)
Several amino acids (including D-ala, Dglu and meso-diaminopimelic acid)

Teichoic acid
Glycerol + phosphate and side chain

Lipopolysaccharide
Lipid A, core polysaccharide, O side chain
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Why do cells stain differentially?

Staining
Treat with crystal violet + iodine, and then
wash with alcohol
Positive cells appear purple; negative cells
appear pink

If cell wall is removed from Gram positive

bacteria
Cells stain as Gram negative
What does it mean?
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Differential Staining
Staining
Peptidoglycan itself does not stain
Peptidoglycan serves as a barrier

Staining
Iodine, helps promote crystal violet retention
Ethanol shrinks the pores (differential effects
on positive and negative cells due to
peptidoglycan thickness)
Ethanol may also extract the lipids and
increase porosity
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Bacterial Cell Wall

Bacteria grouped based on the type of cell
wall:
Gram positive
Staphylococcus aureus
Bacillus anthracis

Gram negative
Escherichia coli
Shigella dysenteriae

Gram non-reactive
Mycobacterium tuberculosis
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Eucaryotes

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Eukaryotes and Prokaryotes

Both have:
cell membrane
DNA as genetic material
ribosomes

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Eucaryotes and Procaryotes (cont.)

Eukaryotes
membrane bounded organelles
multiple chromosomes
80S ribosome
What about cell wall in eucaryotes?

Prokaryotes
lacking membrane bounded organelles
70S ribosome
usually only one chromosome (often circular)
most with 1000-6000 genes (~1-10 million bp)

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Genes and Evolution

Random errors and accidents in copying of
genetic material (nucleotide sequence)
Mutations

Mutations may lead to:

a better gene
no significant change
serious damage

Altered sequence is perpetuated by

mutation and natural selection
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Why have genomes changed?

Genomes have encountered mutations on
a regular basis.
What are the consequences of these
mutations?
deleterious mutations lead to extinction of the cell
mutations leading to better survival are retained

3.5 billion years of such changes indicate

that:
some parts of the genome have been conserved
other parts have changed beyond recognition
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Eucaryotic Cells
Primordial eucaryotic cell was a predator
It required large size with flexible plasma
membrane, cytoskeleton, and a protected
genome in a compartment (nucleus)

All have mitochondria for oxidative

processes (plants have chloroplasts)
Mitochondria originated from an aerobic
eubacteria engulfed by an ancestral cell
Chloroplasts originated as a symbiotic
photosynthetic bacteria
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Eucaryotic Genomes
Genome sizes are much larger than
bacteria
More genes than bacteria
More DNA than protein coding genes
Rich in regulatory DNA

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34
Figure 1-37 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

35
Table 1-1 (part 1 of 2) Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

36
Table 1-1 (part 2 of 2) Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

Eukaryotic cell

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Figure 1-30 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)

Genetic Variations

38

How have genomes evolved?

Intragenic mutations
Gene duplication
Segment shuffling
Horizontal transfer

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Evolution of cells and mutations

Molecular
similarity
The change
leaves a trace
behind to allow
distinction

These
mechanisms
have led to
genetic
innovation
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Gene Duplication and Gene Families

Duplicated genes may undergo mutations
and perform specific genes
Repeated duplication and divergence have given rise to
gene families

Human hemoglobin genes belong to one

such family
Such duplicated genes in the organism are: paralogs

When species split into two lines of

descent:
Duplicated genes in two species are called: orthologs
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Mechanisms of Genetic Variation

Mutations
spontaneous, induced (chemical/physical agents,
viruses), transposons

Sexual reproduction
DNA transfer
Bacteria important because bacteria do not have
traditional sexual reproduction
Horizontal gene transfer (rare in eukaryotes)
Transduction (transport of DNA by bacteriophage)
Transformation (transfer of a naked DNA fragment)
Conjugation (transfer of DNA by direct physical
contact)
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Model Organisms

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Function and Biology of Genes

Genetics and biochemistry are two
complementary approaches to determine
gene function
Sequence comparison allows
determination of conserved domains
Complexity of living organisms have
prompted studies of different aspects in
same organism: MODEL ORGANISM
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E. coli: Model Organism

Gram negative rod
doubles in roughly 20 minutes (under optimal
conditions)
very easy to grow in the lab
some strains are pathogenic; some are normal
flora
E. coli K12 is a commonly used lab strain in
molecular biology labs

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E. coli : Model System

Resides in the gut of human and other
vertebrates
Single circular chromosome
4,639,221 bp
4300 different proteins

Most of our knowledge about replication,

transcription and translation has come from
studies in E. coli
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Other Model Organisms

E. coli studies have been useful to draw
comparisons
Eucaryotic cells/organisms are more complex

Eucaryotic processes have been

investigated by other model systems
Yeast
Worm (C. elegans)
Drosophila
Mouse
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Problem assignment
Why are yeast and mouse important as
model systems?

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Summary
Living cells use different energy sources
Life forms are divided into branches based on similarity
procaryotes and eucaryotes

DNA sequence similarity have led to three branches;

eubacteria, archaebacteria, eucaryotes
Bacteria can be distinguished from other cells by a
distinct cell wall (peptidoglycan)
Cell wall differences are responsible for Gram staining
Genomes have evolved over a period of time by
mutations, duplications, shuffling and genetic transfer
Genetic variations have arisen by transduction,
transformation and conjugation
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