Module 1
The cell and its organelles
Learning Outcomes
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Differentiate between a living organism and non-living forms based on the 7 properties of life
Justify the importance of the 4 main elements (C, O, H, N) that constitute organic molecules.
Define what a cell is and explain what the central dogma is.
List some advantages of multicellularity.
Identify the type of microscopy used based on an image.
Calculate and compare the surface to volume ratio between different organisms.
Predict whether an adaptation can either maximize or minimize the surface to volume ratio.
Name the different structures of prokaryotic and eukaryotic cells.
Differentiate bacterial cells, animal cells and plant cells.
List differences and similarities between prokaryotes and eukaryotes.
Explain the function of each organelle.
Explain how two organelles can be associated based on their cellular functions.
Describe the path of information/molecules through various organelles (i.e. from DNA to protein and its
transport across the cell and to its final destination).
• Determine whether an organelle is an endosymbiont or not based on the number of membranes.
• Summarize the principal chemical reactions occurring in a mitochondrion or a chloroplast.
• Compare the structure and functions of mitochondria and chloroplasts.
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Module 1
The cell and its organelles
1.1 The cell: the unit of life
The cell as unit of life
What is life?
 Life is the natural phenomenon that distinguishes all
organisms from inanimate objects.
All living organisms possess 7 properties:
Heredity and
evolution
Growth and
development
Reproduction
What is a cell?
Cell theory  A cell is the basic structural,
functional, and biological unit of organisms.
It is the smallest unit of life. All cells derive
from pre-existing cells. All organisms are
made of cells (one or more).
Regulation
and
homeostasis
Energy and
metabolism
Cellular
organization
Living organism
Response to
stimuli
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7 properties of life
Virus, prions and viroids are not considered organisms:
• No cellular organization
• No internal metabolism
• No growth or development
100nm
SARS-COV2
Viruses: infectious particle incapable of replicating outside of a cell (RNA or DNA genome + capside made of
protein. Some viruses have a membranous envelope.
Prions: infectious agents (misfolded version of a normal cellular protein).
 increase in number by converting correctly folded versions to more prions
Viroids: small infectious circular RNA molecules. Can replicate using the
replication machinery of their plant host cell.
 Don’t code for any protein and can be transmitted between
cells/individual plants.
PrPSC
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Life on Earth uses carbon
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Highly abundant on earth and in the atmosphere
Small molecular weight and size
Can bind 4 other atoms to form reactive and stable molecules (organic)
Can bind to other carbon atoms: polymerisation
Carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) constitute the
majority of biological molecules:
• Carbohydrates
• Proteins
• Fatty acids
• Nucleic acids, etc.
Human body composition
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Origin of life
Origin of life ~3,500 My ago (prokaryotes)
Hypotheses: Organic molecules necessary for the first step in the origin of life may have been synthesized
from abiotic molecules on the early Earth.
Early atmosphere: methane,
ammonia, hydrogen and some
energy (lightning).
Deep-sea vents:
energy (heat) and
many early organic
molecules.
Clay: mineral catalyst for
the polymerization of RNA
(RNA world). RNA
can also self-replicate.
Stromatolites – 3,500My
(Shark Bay, AUS)
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The cell as unit of life
What is a cell? (Latin “cellula” = small room)
Cell theory
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The cell as unit of life
What is a cell? (Latin “cellula” = small room)
Cell theory
Kangaroo rat
epithelial cells
Pollen grains
Escherichia coli
Neuron cell derived from
stem cell using CRISPR
Macrophage
Cone and rod cells (eye)
Elodea cells and
chloroplasts
Amoeba proteus
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A diversity of cellular functions
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Contain and transmit the genetic material
Acquisition and conversion of energy
Feeding and absorption of nutrients
Structure and support
Communication and response to environmental stimuli
Barrier and defense mechanisms (environmental stresses: biotic and abiotic)
Transport of molecules (osmoregulation, gas exchange)
Reproduction (gametes)
In multicellular organisms, cells are organized in tissues and
tissues are organized in organs.
 Cells, tissues and organs each have very specific functions.
The human body contains ~40 trillion (4×1013) cells…
… and ~10x more microorganisms cells!
Central dogma
Previous theory: one gene = one protein
The central dogma states that: “The sequential information is
transferred from nucleic acid to nucleic acid or from nucleic acid to
protein… but the transfer from protein to protein or from protein to
nucleic acid is not possible”. (Francis Crick, 1956)
James Watson later proposed:
However, Watson’s view is a bit simplistic…
The genetic information encoded in DNA can be transferred to other DNA molecules.
New RNA molecules that have been discovered can transfer their information into DNA.
This last view does not contradict the central dogma stated by
Francis Crick.
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The 3 domains
Origin of life ~3,500 My ago (prokaryotes)
Eukaryotes: 1,800 My ago
Phylogenetic tree from
ribosomal protein sequences
(Hug et al 2016)
3 domains: Eukarya, Archaea and Bacteria
Archaea: prokaryotes that are not bacteria (extremophiles: acidic,
hot, high salinity environments, methanogens)
~11,000,000 species
Saccharomyces cerevisiae
~50,000 species
~700,000 species
Pyrococcus furiosus
COMMON
ANCESTOR
OF ALL LIFE
Escherichia coli
Ribosomal proteins are very
critical for protein synthesis
and are under very strong
selection (mutations that disrupt their
amino-acid sequence are selected out)
 Their sequences evolve slowly
 More mutations have accumulated
between more distant lineages
 These “highly conserved” proteins help
resolve the root of the tree of life
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Multicellularity
In eukaryotes  evolved around 1,200 My ago… but evolved 25 times independently in various lineages!
Some groups have lost their ability to grow into multicellular organisms.
Some advantages of multicellularity:
• Increase in the surface area for diffusion
• Longer lifespan
• Specialization of cells into cell types, tissues and organs
• Protection, feeding, locomotion, reproduction
• Colonial hypothesis: cooperation of unicellular organisms of the same species (failure to separate or
separating and rejoining)  cellular specialization
Ex: colonies of cyanobacteria
Photosynthetic cells
Nitrogen fixing cells (heterocyst)
Anabaena circinalis
Ex: colonies of green algae
 50,000 cells that are
specialized in 2 layers
Some Volvox species are
considered multicellular!
Volvox sp.
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Eukaryotes
Protists are all of the
eukaryote organisms
that are neither fungi,
plants or animals
Paramecium caudatum
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Module 1
The cell and its organelles
1.2 Cell size and microscopy
Cells vary in size
Blue whales
neurons can be
30m long!
Robert Hooke
Hooke’s microscope
Mucor mucedo (fungus)
Eukaryotes:
10-100µm
Lens
Pin supporting
the specimen
Antoni van Leeuwenhoek
Microscope (x270) - 1668
Most cells range
from 1µm to 100µm
Prokaryotes:
1-5µm
Bacteria and their movement
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Microscopy
Light microscope:
The light goes through the
specimen and the image
is magnified by refraction
through a lens. The specimen can
be observed alive in most cases.
Transmission Electron Microscope (TEM):
A beam of electrons goes
through the specimen and
can reveal internal structures.
Requires very thin slices of
the specimen hardened in resin
or frozen, stained with heavy
metal and cut using a microtome.
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Microscopy
Electron gun (1000,000 volts)
Empty chamber (vacuum)
Electrons beam
Scanning Electron Microscope (SEM):
A beam of electrons scans the surface
of the specimen coated with gold (high
conductivity). Secondary electrons
liberated by the sample are detected
and converted into an electric signal
for imaging.
Deflection coils
Scanning of the electron
Beam on the object’s surface
Deflected electrons
Sample
Detector (camera)
Computer processing
3D image
Fluorescence microscope:
The specimen is labelled with a fluorescent
marker: green fluorescent protein (GFP),
fluorescent chemical compound, antibody
tagged with a fluorescent molecule… which
is then excited at a very specific wavelength.
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Surface to volume ratio of cells
With increasing cell size the cell volume increases more rapidly
than its surface area!
𝑆
 bigger cells have a smaller surface to volume ratio
𝑉
Cell surface area = 4πr2
4
Cell volume = πr3
3
Because diffusion across the membrane depends on its surface area, exchanges
between the cell and the environment are more efficient for smaller cells.
Microvilli
Ex: Villi of epithelial cells in the
lumen of the small intestine
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Surface to volume ratio of cells
With increasing cell size the cell volume increases more rapidly
than its surface area!
𝑆
 bigger cells have a smaller surface to volume ratio
𝑉
Cell surface area = 4πr2
4
Cell volume = πr3
3
Because diffusion across the membrane depends on its surface area, exchanges
between the cell and the environment are more efficient for smaller cells.
Time to 95% equilibration of O2 by
diffusion across the plasma membrane:
x
Length (x)
Time
0.1 mm
0.067 s
1 mm
6.7 s
1 cm
11 min 10 s
1m
78 days
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Surface to volume ratio of cells
With increasing cell size the cell volume increases more rapidly
than its surface area!
𝑆
 bigger cells have a smaller surface to volume ratio
𝑉
Cell surface area = 4πr2
4
Cell volume = πr3
3
Because diffusion across the membrane depends on its surface area, exchanges
between the cell and the environment are more efficient for smaller cells.
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Module 1
The cell and its organelles
1.3 Differences between prokaryotes and eukaryotes
Differences prokaryotes/eukaryotes
Bacterial cell
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Similarities between prokaryotes/eukaryotes
• Genetic information encoded in DNA
The genetic code is not universal.
Variations between species.
Mitochondria have a different code.
• Plasma membrane made of
a bilayer of phospholipids
Role: selective barrier,
communication, adhesion,
cell structure…
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Similarities between prokaryotes/eukaryotes
• Similar mechanisms for…
- transcription and translation of genetic information, including
similar ribosomes
- photosynthesis (cyanobacteria and plants)
- synthesizing and inserting membrane proteins
• Presence of a cytoskeleton (network of filaments with mechanical,
transport and signalling functions), but the proteins differ between
prokaryotes (FtsZ and MreB) and eukaryotes (actin, tubulin, keratin).
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Similarities between prokaryotes/eukaryotes
• Similar process for the conversion of chemical energy into ATP:
prokaryotes: plasma membrane
eukaryotes: mitochondrial membrane
• Shared metabolic pathways (ex: glycolysis and citric acid cycle)
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Differences prokaryotes/eukaryotes
Cytoplasm: total content of the cell bounded by the plasma membrane
 in eukaryotes, the cytoplasm excludes the nucleus!
Cytosol: internal fluid containing organic molecules, proteins, metabolic waste, etc.
In prokaryotes:
• Absence of nucleus.
• Presence of a nucleoid (non-membrane-bounded region
where the circular chromosome is concentrated).
• Absence of organelles (membrane-enclosed structures with
specialized functions).
• The cytoplasm is therefore made of the cytosol.
In eukaryotes:
• The cytoplasm includes the cytosol, organelles, some
inclusions (particles of insoluble substances), and
excludes the nucleus.
• Presence of a nucleus with linear chromosomes, made of
chromatin (DNA + histone proteins).
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Differences prokaryotes/eukaryotes
Cell walls containing peptidoglycan (bacteria), pseudomurein (archaea), cellulose (plants), absent in animals
Ex: Staphylococcus aureus
Ex: Escherichia coli
Bacteria plasma membrane and cell wall
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Differences prokaryotes/eukaryotes
Cell walls containing peptidoglycan (bacteria), pseudomurein (archaea), cellulose (plants), absent in animals
Strong durable protection
and support in some cells,
added between the
plasma membrane and
the primary cell wall when
a cell stops growing
Thin and flexible
Thin layer of pectin
(sticky polysaccharide)
which glue adjacent cells
together
Plants plasma membrane and cell
wall made of cellulose
The cell wall in plants
maintains the shape of the
cell, prevents excessive
water uptake and acts
as a barrier to pathogens
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Differences prokaryotes/eukaryotes
Cell walls containing peptidoglycan (bacteria), pseudomurein (archaea), cellulose (plants), absent in animals
Extracellular matrix (ECM) of animal cells: network of glycoproteins, polysaccharides and proteoglycan.
 bonded covalently to short chains of sugar (e.g. collagen ~40% of all proteins in the human body).
Collagen fibers are embedded in a network of
proteoglycan (core protein bonded covalently
to polysaccharides).
Fibronectin are proteins that attach both
the ECM and integrins (transmembrane
proteins) which are themselves attached
to the microfilaments of the cytoskeleton.
Integrins can transmit (integrate) information
between the ECM and the cytoskeleton.
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Differences prokaryotes/eukaryotes
• Reproduction and cell division:
Prokaryotes: asexual through
binary fission (simple cell division)
into two identical daughter cells.
Eukaryotes: sexual reproduction
requiring meiosis and fertilization
Note that many eukaryotes can in
addition reproduce asexually.
Mitosis: eukaryotic cell division using a microtubule-containing
mitotic spindle that separates chromosomes
• RNA synthesizing enzymes (RNA polymerases): 1 in prokaryotes, and 3 in eukaryotes
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Differences prokaryotes/eukaryotes
Flagellum: long cellular appendage specialized for locomotion.
Eukaryotes: projects from the cytoskeleton
and covered by the plasma membrane.
Prokaryotes: Flagellum made of
flagellin and inserted in the
plasma membrane
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Features only found in eukaryotes
• Complex chromosomes composed of DNA and associated proteins (histones) that
are capable of compacting into mitotic structures (used in mitosis, which is absent in prokaryotes)
• Membranous cytoplasmic organelles (includes endoplasmic
reticulum, Golgi complex, lysosomes, endosomes, peroxisomes…)
• Specialized cytoplasmic organelles for aerobic respiration
(mitochondria) and photosynthesis (chloroplasts)
• Proteins and filaments of the cytoskeletal system (actin filaments,
intermediate filaments and microtubules) as well as motor
proteins. All those are very different in prokaryotes.
• Ability to ingest particulate material by enclosure within plasma
membrane vesicles (phagocytosis)
• Presence of two copies of genes per cell (diploidy), one from each
parent (sometimes more, ex: polyploidy in plants)
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Module 1
The cell and its organelles
1.4 Organelles I: Nucleus, Endoplasmic Reticulum, Golgi
Apparatus, Lysosome, Peroxisome, Vacuole
Organelles
Organelles: membrane-enclosed structures with specialized functions,
suspended in the cytosol of eukaryotic cells.
Prokaryotes: no compartmentalization (no organelles!).
Organelles can
move within the
cell following the
cytoskeleton
tracks.
Their size
and number
can depend
on the
metabolic activity
of the cell.
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Nucleus
Nucleus: organelle in eukaryotes containing genetic material (chromosomes). Some genes on mitochondrial
(and chloroplast) chromosomes.
Red blood cells in human do not have nucleus!
The nucleus is surrounded by the nuclear envelope: double membrane (two
bilayers of lipids) supported by a nuclear lamina (network filamentous proteins)
Nuclear pore complexes regulate the entry and exit of nucleic
acids and proteins.
Chromatin: complex of DNA + histone proteins making up
chromosomes in eukaryotes. Can condense (coil) during cell division.
In human: 46 chromosomes (2n = 46)
 22 pairs of autosomal chromosomes
 1 pair of sexual chromosomes (XY)
Gametes have a single set of each!
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Nucleus
Nucleolus: Specialized structure in the nucleus, consisting of chromosomal regions
containing ribosomal RNA (rRNA) genes along with ribosomal proteins imported from the cytoplasm.
 site of rRNA synthesis and ribosomal subunit assembly with the rRNA.
Each subunit is linked to an rRNA and exits the nucleus through the
nuclear pores. Both subunits will assemble in the cytoplasm
to form a ribosome.
Ribosomes then use mRNA (messenger
RNA, synthesized in the nucleus and
encoding the genetic information) to
synthesize proteins in the cytoplasm.
Ribosomes are free in the cytosol or
bound to the outer layer of the endoplasmic
reticulum depending on the destination of the protein synthesized.
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Endoplasmic Reticulum (ER, “net within cytoplasm”)
Endoplasmic Reticulum (ER): membranous network, continuous with the outer nuclear membrane.
Rough ER: ribosome-studded
 Synthesis of proteins that are secreted by the cell (ex: glycoproteins) or sent to other parts of the cell.
These secretory proteins are directed during translation into the ER lumen and transported within transport
vesicles.
The ER can synthesize phospholipids to form/replace new membranes.
Membrane proteins are also inserted
directly into the ER membrane before
they are also sent to various parts
of the cell.
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Endoplasmic Reticulum (ER, “net within cytoplasm”)
Smooth ER: ribosome-free and contains many enzymes responsible for many metabolisms.
 Synthesis of lipids, phospholipids, steroids (ex: sexual hormones), cholesterol, carbohydrate metabolism
 Detoxification (toxins, drugs, ethanol…)  CYP450 (Cytochrome 450) enzymes that can break down drugs
 Calcium storage (after the muscle contraction)  sarcoplasmic reticulum of muscle cells
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Golgi apparatus (GA)
The Golgi apparatus is a trafficking center: manufactures, receives, sorts, modifies, ships many molecules.
Vesicles arrive from the ER, fuse with the GA membranes and leave the GA (cis-to-trans direction)
Proteins can mature in the GA: posttranslational modifications (PTMs). 88% of PTMs are either
phosphorylation (addition of phosphate), glycosylation (addition of carbohydrate) or acetylation (addition
of an acetyl). Glycoproteins and phospholipids can also be modified, stored and shipped in the cell.
Polysaccharides can also by synthesized or modified in the GA.
Ex: glycosylation of an oligosaccharide
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Lysosome
Lysosome: digestive organelle that contains hydrolytic enzymes (digestion of macromolecules)
Its content is very acid and lytic enzymes work at a low pH (between 4.5 and 5).
Lysosomes derive from the Golgi apparatus
Fusion of lysosomes with
phagocytosis vesicles
 digestion of preys/pathogens
into simple sugars or amino acids
then released in the cytosol
Phagocytosis
Lysosome
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Peroxisome
The peroxisome is a single-membrane oxidative organelle that contains enzymes (often in
the form of crystals) that remove hydrogen atoms from substrates and transfer them to oxygen (O2)
 producing hydrogen peroxide (H2O2)
Role:
• Break fatty acids down into smaller molecules for cellular respiration (mitochondria)
• Detoxification by oxidizing alcohol and other harmful compounds.
H2O2 very reactive/toxic… but converted to H2O before exiting the peroxisome.
Glyoxisomes (a type of peroxisome in plants) allow seedlings to grow by
breaking down the stored fatty acids.
 allowing growth before photosynthesis!
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Vacuole
Vacuole: Large vesicles derived from the ER/GA.
Semi-permeable membrane (high selectivity)
 transport inside of only very specific molecules.
Role:
• Storage of nutritious molecules (proteins, carbohydrates…),
poisonous molecules, lytic enzymes, pigments, water and ions
(osmotic pressure).
• Cell growth, structural support and tendrils (climbing
stems) through the increase in cell volume (turgor
pressure from hydrostatic pressure of the vacuole on
the cell wall).
Elodea sp.
Vacuoles can also produce/store many molecules
of industrial interests (genetic engineering).
Ex: betaxanthin (pigment) as an indicator of dopamine production in yeast cells!
DeLoache et a. 2015
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Module 1
The cell and its organelles
1.5 Organelles II: Mitochondria and Chloroplasts
Endosymbiosis
Mitochondria and chloroplasts derived from prokaryotes integrated
inside another prokaryote through endosymbiosis (1,800 My).
Endosymbiosis: relationship between two species in which
one organism lives inside the cell or cells of another organism.
Mitochondrion, plastid: organelles possessing its own membrane
circular DNA, their own transcription/translation proteins,
ribosomes/membrane proteins similar to those of bacteria.
Serial endosymbiosis:
• The mitochondrion originates from the phagocytosis of (or the
parasitism) from an aerobic bacterium by an archaea cell
• The chloroplast originates from the phagocytosis of a
photosynthetic bacterium by eukaryote.
 Benefits: the cell gains a new metabolic system
(ex: aerobic respiration with increasing O2 concentrations).
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Membranes
The plasma membrane constitutes a selective barrier with the environment.
Mitochondria and chloroplasts are organelles with a double membrane (derived from endosymbiosis)
Mitochondria
Chloroplast
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Mitochondrion
Double membrane-bound organelle that converts chemical energy
acquired from the environment (ex: glucose) into chemical energy
that is directly usable by the cell (ATP).
This is done through cellular respiration:
(here aerobic respiration = in the presence of oxygen)
Chemical energy is stored in the bounds between atoms:
• Between atoms of carbon
• Between phosphate groups:
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Mitochondrion
Present in (almost) all eukaryotic cells (up to thousands mitochondria).
Infoldings of the inner membrane (cristae) separate the
intermembrane space from the mitochondrial matrix.
 increase of the surface area for cellular respiration
 enzymes necessary for cellular respiration
are within the intermembrane space, others
are embedded in the inner membrane
Ex: ATP synthase
Mitochondria possess their own DNA
and ribosomes.
Some genes were transferred to the nucleus.
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The cell as unit of life
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Chloroplast
Double membrane-bound organelle that converts solar energy acquired
from sunlight into chemical energy (ex: glucose)... that can then be converted
by the mitochondrion into energy that is directly usable by the cell (ATP).
This is done through photosynthesis:
An intermembrane space separates both
membranes of the chloroplast.
Thylakoids: membranous flat and interconnected
sacs inside the chloroplast and that are stacked (granum) and
that contain the photosynthetic pigments (chlorophylls).
Thylakoids float inside the stroma (fluid containing the
chloroplast DNA, ribosomes and many enzymes).
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Chloroplast
Chloroplasts can grow, divide and move within the cell.
The chloroplast is a specialized member of a family of closely related
plant organelles called plastids:
• Chloroplasts (photosynthesis)
• Chromoplasts (fruit and flower pigmentation)
• Amyloplasts: storage of starch (amylose) in roots and tuber
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Plant cell
Note that plant cells do possess mitochondria to convert the
chemical energy produced from photosynthesis into ATP!
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Photosynthesis and cellular respiration
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