Introduction to the Cell:

Cells, Genomes, and the

Diversity of Life
MBG201-Fall 2023
Gülistan MEŞE ÖZÇİVİCİ

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 All Living Things Share the Same Machinery for
Their Most Basic Functions
 > 2 million described
species on Earth

 Each species is able to

reproduce  transmission
of hereditary information to
the progenies

 Unicellular and
multicellular organisms are
all derived from the division
of a single cell

 Only living things are

able to produce progenies
that resemble to their
parents

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Figure 1-1 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 All Cells Store Their Hereditary Information in the
Form of Double-Strand DNA Molecules
• store hereditary
information in the form
of DNA
• Use the four-letter
alphabet of A, T, C and
G.

• A piece of DNA from an

organism can be read
by another one.

- universal alphabet.

• DNA - use a template to

make a new single strand
during replication by
templated polymerization

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 All Cells Transcribe Portions of Their DNA into RNA
Molecules
• DNA - the information bearing
molecule

• RNAs and proteins - functional

manifestation of genetic information

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Figure 1-4 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 RNA Molecules can Form Secondary Structures
RNA

• Single stranded
• Flexible backbone
• Bend back on itself

• Formation of secondary
structures

• Selective binding to specific

molecules

• Catalysis of chemical changes

in the molecule
Hepatitis delta virus RNA catalyzes RNA strand cleavage
• Catalytic RNA- ribozymes

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Figure 1-6 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 All Cells Use Proteins as Catalysts
Proteins:

• Functional subunit of the

cells

• Formed from amino acids

• unique function determined by their
sequences
• Autocatalytic, self producing behavior between
proteins and nucleotides

http://www.bothbrainsandbeauty.com/page/3, http://www.stat.rice.edu/~marina/research.html 6
Figure 1-7a, 7b Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
All Cells Translate RNA into Protein in the Same Way

• Ribosomes - the protein factories in all cells

• Each protein is encoded by a specific gene 7
 Life Requires a Continual Input of Free Energy

 Cell growth, replication and many molecular mechanisms – in need of free energy

 Cells must take in free energy and raw materials (sugar, nucleotides, amino acids)
from their environment

 All cells function as biochemical factories

 ATP is used as both building block for the synthesis of DNA and RNA and as the
carrier of free energy for many cellular events.

 Different cells can use different energy sources: organic molecules, light, inorganic
molecules

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All Cells Are Enclosed in a Plasma Membrane Across
Which Nutrients and Waste Materials Must Pass
 Maintain the integrity of cells

 Selective barrier - control the passage of

molecules in-and-out of the cell

 Amphiphilic - Spontaneous formation of

enclosed lipid bilayer in water

 Specialized proteins- the transfer of specific

molecules

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Cells Operate at a Microscopic Scale Dominated by
Random Thermal Motion
Thermal or Brownian motion-
spontaneous movements
 Drive diffusion
 Rates of biochemical
reactions

Membrane protrusion driven by Brownian ratchet

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A Living Cell Can Exist with 500 Genes

Mycoplasma genitalium

525 genes- 580070 nucleotide

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 Genome Diversification and the Tree of Life
Living in all environmental conditions- darkest depths of the ocean to the hot
volcanoes, to the frozen surfaces of the Antarctic

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The Tree of Life Has Three Major Domains:
Eukaryotes, Bacteria, and Archaea
• physical structure (how they look)
• genetic similarities (DNA)

rRNAs comparison 13
Eukaryotes Make Up the Domain of Life That Is Most
Familiar to Us
• Eukaryotes – truly
nucleated
• Larger
• Bigger genomes

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 On the Basis of Genome Analysis, Bacteria Are the
Most Diverse Group of Organisms on the Planet

• Enormous diversity
• Diverse ecological niches
• Variable chemical
capabilities
• Variable energy source-
organic, inorganic, light
Beggiatoa-oxidize H2S
Photosynthetic bacteria 15
Archaea: The Most Mysterious Domain of Life
• Small
• Lack membrane bound
organelles
• Different from bacteria
• in cell wall
composition
• biochemical
reactions
• genome similarities to
eukaryotes
• Predominant life form
in soil and seawater
• Recycling of nitrogen
and carbon

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 Organisms Occupy Most of Our Planet
• Earth total mass - 550 gigatons of carbon

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 Cells can be Powered by a Wide Variety of Free-
Energy Sources
• Organotrophics: use
organic molecules

• Phototrophics: use
sunlight and produce O2

• Lithotrophics: use
inorganic chemicals,
organisms live in
inhabitable environments,
e.g bacteria living in
hydrothermal vents
Complex ecosystems
• Molecules of living organisms - H, C, N, O, S and P.

• Some organisms cannot get these elements directly from their environment, need
other organisms that can incorporate them in organic molecules.

• Animals gets fixed CO2 from plants that get their nitrogen from nitrogen-fixing
bacteria 18
 Genomes Diversify Over Evolutionary Time,
Producing New Types of Organisms
• Outcomes of changes in nucleotide sequence-?

Genetic information conserved since the days of the last universal common ancestor
of all living things- ribosomal RNA (rRNA)

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New Genes Are Generated from Preexisting Genes

Gene Duplications Give Rise to

Families of Related Genes Within a
Single Genome

Families of
evolutionarily related
Four modes of genetic innovation and their
genes in the genome of
effects on the DNA sequence of an
Bacillus subtilis
organism.
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Gene Duplications Give Rise to Families of Related
Genes Within a Single Genome
Types of gene homology based on different evolutionary
pathways

Likely to have the same May have different

function in the two function within the species
species
The function of a gene can often be deduced from its nucleotide sequence 21
More Than 200 Gene Families Are Common to All
Three Domains of Life

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 Eukaryotes and the Origin of the Eukaryotic Cell
Eukaryotic Cells Contain a Variety of Organelles

• ~50 of cytoplasm- membrane enclosed

organelles
• Rest- cytosol
• Biomolecular condensates- membraneles
organelles
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 Eukaryotes and the Origin of the Eukaryotic Cell
Mitochondria Evolved from a Symbiotic Bacterium Captured by an Ancient Archaeon

A scanning
electron
micrograph of an
Asgard archaeon
in culture A mitochondrion

A possible model
for some early
steps in
eukaryotic cell
evolution
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 Eukaryotes and the Origin of the Eukaryotic Cell
Eukaryotes Have Hybrid Genomes

A model for the evolution of eukaryotic cells in the tree of life

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 Eukaryotes and the Origin of the Eukaryotic Cell
Eukaryotic Genomes Are Big

Model organisms and their genomes

Genome sizes compared

Eukaryotic genomes are rich in regulatory DNA- formation and function of

complex multicellular organisms

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Eukaryotes and the Origin of the Eukaryotic Cell
Eukaryotic Genomes Define the Program of Multicellular Development

Some model organisms and their genomes

Cell types can vary
enormously in size and
shape 27
 Eukaryotes and the Origin of the Eukaryotic Cell
Many Eukaryotes Live as Solitary Cells

ciliates amoeba
ciliates An assortment of
ciliates
single-cell eukaryotes.
heliozoan the scale bar
represents 10 µm in
each

dinoflagellate
euglenoid

A single-cell eukaryote that eats other cells

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 Eukaryotes and the Origin of the Eukaryotic Cell
Many Eukaryotes Live as Solitary Cells

A eukaryotic tree of life based on genome comparisons 29

 Model Organisms
Mutations Reveal the Functions of Genes
• Testing gene function? biochemistry and genetics

An alteration in organism
shape resulting from a
gene mutation

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 Model Organisms
Molecular Biology Began with a Spotlight on One Bacterium and Its Viruses
• Escherichia coli (E.coli)

- Live in the gut of human and other

vertebrates
- Adapt to various conditions so easy to grow
in lab
- Easy to propagate
- Simple nutritional requirements
- Small genome size: ~ 4300 proteins
- Rapid evolution through mutation and The T4 bacteriophage
natural selection

Studies:
- DNA replication
- Transcription
-Gene expression
- Protein synthesis

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 Model Organisms
A Yeast Serves as a Minimal Model Eukaryote
• Saccharomyces cerevisiae
• Single cell fungi
• Easy and rapid growth in the lab
• Cell wall
• Small genome compared to other
eukaryotes
• Vegetative or sexual reproduction

• Its genome is completely sequenced:

• ~6300 protein

DNA replication
Transcription
RNA processing
Protein sorting
Cell division

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 Model Organisms
Arabidopsis Has Been Chosen as a Model Plant

• Close evolutionary relationship between all

flowering plants

• Can grow indoors in large amounts

• Short breeding time
• Many offsprings

• Important for plant biology, development and

differentiation

• Its genome is completely sequenced with 140

million nucleotides

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 Model Organisms
The World of Animal Cells Is Mainly Represented by a Worm, a Fly, a Fish, a Mouse,
and a Human

Caenorhabditis elegans
• Small worm,
• The first multicellular organism
to have its complete genome
sequence determined Fruit Fly Drosophila melanogaster
• Survive in freezer indefinitely • The oldest model organism
• Simple body plan • Easy and cheap to grow in the lab,
• Short life cycle, • Short life cycle
• ~20000 proteins • ~14000 genes
• Many mutant strains • Many mutant strains
• Genetic studies, development • Genetic studies, vertebrate
and differentiation, cell development and differentiation
division, cell death 34
 Model Organisms
The World of Animal Cells Is Mainly Represented by a Worm, a Fly, a Fish, a Mouse,
and a Human
The Frog and the Zebrafish Provide
Highly Accessible Vertebrate Models
• Xenopus laevis
• Transparent embryos
• Easy to manipulate embryos:
injection of gene of interest
• Early vertebrate development

• Zebrafish, Danio rerio- tropical fish

• Genetic studies
• Transparent embryos
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 Model Organisms
The World of Animal Cells Is Mainly Represented by a Worm, a Fly, a Fish, a Mouse,
and a Human
The mouse, Mus musculus is the predominant mammalian
model organism
• Mammals are closely related with each other- share the
same set of organization
• Small
• Rapid breeder
• Molecular genetic studies
• Advances in genetic technologies

Times of divergence of
different vertebrates
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 Model Organisms
The COVID-19 Pandemic Has Focused Scientists on the SARS-CoV-2 Coronavirus

SARS-CoV-2
• ssRNA genome
• Packaged in a protein coat
• 29 proteins

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 References
Chapter 1
Molecular Biology of the Cell, Seventh Edition

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