LESSON 1

THE CELLS

FACTS:

 The average human being is composed of around 100 trillion individual cells.
 It would take as many as 50 cells to cover the area of a dot on the letter “i”

BIOSPHERE – the part of earth that contains all ecosystems

ECOSYSTEM – community and its nonliving surroundings

COMMUNITY – populations that live together in a defined areas

POPULATION – group of organisms of one type that live in the same area

ORGANISM – individual living thing

GROUPS OF CELLS – tissues, organs and organ systems

CELLS – smallest functional unit of life

MOLECULES – group of atoms; smallest unit of most chemical compounds

AUTOTROPHIC or also called as producers – an organism that can produce its own food
using water, light or other chemicals.

HETEROTROPHIC – an organism that eats other plants or animals for energy and nutrients

Hetero – other

Trophe – nourishment

BIOSYNTHESIS – the production of a chemical compound by a living organism

RIBOSOME – a cellular particle made of RNA and protein that serves as the site for protein
synthesis in the cell.

ROBERT HOOKE – English father of Microscopy

GARTH NICOLSON – a biochemist who made the scientific model for cell membrane known
as Fluid Mosaic Model
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CELL THEORY: ITS DEVELOPMENT

Year of Discovery Scientist Contribution

1590 Hans & Zacharias Dutch; developed the first
Janssen compound
microscope by combining 2 lenses
in a tube
1665 Robert Hooke English; discovered small, hollow
compartments in a cork of an oak
tree --- cells
1675 Anton van Dutch; observed tiny living
Leeuwenhoek organisms
from rainwater, saliva, blood ---
animalcules
1838 Matthias Schleiden German; suggested that plants
were made up of cells
1839 Theodor Schwann German; suggested that animals
are made up of cells
1840 Jan Evangelista Purkinje Czech; named the cellular content
‘protoplasm’
1855 Rudolf Virchow German; suggested that all cells
come from cells
CELL THEORY: ITS PRINCIPLES

 All living things are composed of one or more cells.

(Schleiden & Schwann)(1838-39)
 The cell is the basic units of structure and function of all organisms.
(Schleiden & Schwann)(1838-39)
 All cells arise only from pre-existing cells.
(Virchow)(1858)

CELL is described:

 as the basic structural and functional unit of life

 simplest entity capable of carrying out life’s processes
 can exist alone (unicellular) or as a complex organism (multicellular)
 to be composed primarily of C, H, O, N
 minor elements --- Ca, P, K, S, Na, Cl, Mg, I, Fe
 trace elements --- Cr, Co, Cu, F, Mn, Mo, Se, Si, Sn, V, Zn
 to contain over 60 percent water --- homeostasis (buffering effect)
 to have carbohydrates, lipids, proteins and nucleic acids as the major
biomolecules
 to vary in size --- ranges from 0.2μm to 2mm
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 to vary in shape --- fixed or variable

TABLE 1. VARIOUS CELL SHAPES AND THEIR EXAMPLES.

CELL SHAPE Example

Amoeba, Leucocytes, Myxomycytes

 Variable cells
 Fixed cells
 Spherical cells Egg of many animals

 Flattened cells Squamous epithelium, endotheliums and

upper layer of epidermis

 Cuboidal cells Thyroid gland follicles

 Columnar cells The cells lining the intestine

 Discoidal cells Erythrocytes

 Spindle shaped cells Smooth muscle fibers
 Elongated cells Nerve cells
 Branched cells Pigment cells of skin

PROKARYOTIC & EUKARYOTIC CELL: Similarities and Differences

PROKARYOTIC

 Greek pro (before) + karyon

(nucleus)
 ○without true nucleus
 no organelles
 has a NUCLEOID region

EUKARYOTIC

 Greek eu (true) + karyon

(nucleus)
 with true NUCLEUS
 with ORGANELLES
 smaller
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PROKARYOTIC EUKARYOTIC

with NUCLEOID COMMON with NUCLEUS

NO nucleus plasma membrane with organelles

NO organelles cytoplasm

DNA (genetic material)

ribosomes

CELL STRUCTURE PROKARYOTES EUKARYOTES

SIZE SMALLER (1-10mm in LARGER (10-100mm in
diameter) diameter)
NUCLEAR ENVELOPE ABSENT PRESENT
CELL WALL MADE UP OF MADE UP OF CELLULOSE
PEPTIDOGLYCAN WHEN WHEN PRESENT
PRESENT
MEMBRANE-BOUND ABSENT PRESENT
ORGANELLE
NUCLEAR MATERIAL SINGLE LOOP OF CIRCULAR DOUBLE-STRANDED DNA
DNA ARRANGED IN A
DOUBLEHELIX STRUCTURE
RIBOSOME SMALL (70S) LARGE (80S)
S = SVEDBERG / SUBUNIT
CYTOSKELETON ABSENT PRESENT
MITOCHONDRIA ABSENT PRESENT
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PROKARYOTIC VS EUKARYOTIC

PLASMA MEMBRANE

 structural barrier separating the cell from the outside environment; with protective
and regulatory functions

CELL MEMBRANE

 Gateway to the Cell

 Acts as a boundary
 Controls what enters and leaves cell
 Regulates chemical composition
 Maintains homeostasis

CYTOPLASM

 space in the cell where most cellular activities take place --- “factory area”
 contains an intracellular matrix called cytosol where all other cellular components
are suspended
 organelles --- membrane-bound structures in eukaryotic cells
 inclusions --- non-permanent and inactive substances/materials in the cell (i.e. fat
globules, crystals)

DNA (genetic material)

 “blueprint” of an organism
 carries all the information necessary for the growth, development and survival of an
organism
 Ribosomes
 small non-membrane bound structures that act as sites for protein synthesis
in the cell

PHOSPHOLIPID BILAYER

 In water, phospholipids spontaneously form a stable two layer sheet called a

phospholipid bi-layer

LIPIDS

 Organic compounds
 Fats + Oils
 Non-polar
 Insoluble in water or (Not attracted to water)
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PHOSPHATE HEAD

 Polar
 Water-soluble or (Attracted to water)

PROKARYOTIC CELL

1. CAPSULE
 a sticky outer layer that provides protection
2. CELL WALL
 a structure that confers rigidity and shape to the cell
3. PLASMID
 A genetic material
 Extra chromosomal ring of DNA
4. NUCLEOID
 A DNA-containing region within the cytoplasm
5. PILUS (phili)
 A hair-like appendage that functions in adhesion
6. FLAGELLUM
 Facilitates movement of bacteria

ORGANELLES: Similarities and Differences

 Membrane-bound structures performing a specific function in eukaryotic cells

 distribution of work in the cell --- maximizes time and space

NUCLEUS

 structure
 double-membraned structure with nuclear pores that connect the nuclear
components to the cytoplasm
 control center of the cell
 function
 directs RNA and protein synthesis
 stores the genetic information (DNA)

NUCLEOLUS

 structure
 spherical organelle within the nucleus
 function
 assembles ribosomes
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ENDOPLASMIC RETICULUM

 structure
 network of internal membranes (endomembrane system)
 divided into 2 regions:
 ROUGH ER --- with ribosomes
fxn: protein synthesis
 SMOOTH ER --- w/out ribosomes
fxn: lipid synthesis, regulates calcium levels
 function
 compartmentalizes the cell creating a greater surface area for cellular processes
to proceed
 serves in the transport of cellular products via the formation of vesicles

GOLGI BODIES

 structure
 stacks of flattened membranous sacs called cisternae
 cis face --- accepts incoming transport vesicles from the ER
 trans face --- releases secretory vesicles containing the finished product
 function
 modifies and packages cellular products

LYSOSOME

 structure
 small spherical bodies containing digestive or acidic hydrolytic enzymes
 function
 digests macromolecules, cellular debris, old organelles and foreign substances

PEROXISOME

 structure
 small spherical bodies containing oxidase enzymes
 function
 neutralizes toxic substances
 breaks down fatty acids

VESICLES

 structure
 membrane-bound sacs
 function
 store and transport substances
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VACUOLE

 structure
 membrane-bound sacs
 in animals, there are many but small in size
 in plants, there is only one but big central vacuole
 function
 store water, enzymes, pigments, waste products

MITOCHONDRION

 structure
 hotdog-shaped structure with smooth outer membrane, folded inner membrane
and many respiratory enzymes
 intermembrane space separates the outer and inner membranes
 folds of the inner membrane are called cristae
 matrix is the space within the inner membrane
 have small amount of dna
 function
 produces ATP (aerobic respiration)

CHLOROPLAST

 structure
 double-membraned, green oval structure with stacks of sac-like structures within
 thylakoid refers to the sac-like structure containing pigments such as chlorophyll
and carotenoids
 thylakoids stack together to form a granum
 function
 facilitate food production in photosynthetic organisms

CYTOSKELETON

 structure
 network of protein filaments including microfilaments, intermediate filaments,
microtubules
 cilia and flagella --- motility
 centriole --- anchor and assemble spindle fibers in animal mitosis
 function
 provides structural support and movement (in some) to the cell

ENZYME
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 Enzymes are proteins that help speed up chemical reactions in our bodies. Enzymes
are essential for digestion, liver function and much more.
 Catalyze all kinds of chemical reactions that are involved in growth, blood
coagulation, healing, diseases, breathing, digestion, reproduction, and many other
biological activities.

CELL WALL

 structure
 rigid structure in plants and members of the kingdom fungi made up of cellulose
or chitin, respectively
 function
 provides structural support to the cell

ANIMAL VS PLANT CELL: A Comparison

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CELL STRUCTURE ANIMAL CELL PLANT CELL

CELL WALL ABSENT PRESENT
CHLOROPLAST ABSENT PRESENT
VACUOLES USUALLY NUMEROUS AND SINGLE AND LARGE
SMALL (USUALLY AT THE CENTER OF
THE CELL)
CENTRIOLES PRESENT ABSENT
CILIA and FLAGELLA PRESENT ABSENT IN FLOWERING
PLANTS BUT PRESENT IN
FERNS, CYADS AND
BRYOPHYTES

CELL MODIFICATION

CELL SURFACE MODIFICATION

 A type of apical (apex) surface that has modifications such as microvilli

(microvillus) or cilia.

MICROVILLI

 Increase the surface area and secrete substances “shaggy hairs”; finger-like
extensions of the plasma membrane function in absorption of nutrients.

NERVE CELLS

 Which are elongated, facilitate the transmission of impulses from the brain and
the spinal cord to the different parts of the body.

RED BLOOD CELLS

 Have a biconcave disc shape and are highly deformable. This allow for easy
movement through blood vessels. Has 2-3 Micrometer.

SPERM CELLS

 Have tail, flagellum which propels it toward the egg cell for fertilization.

CILIA

 Hair like projections on the cell surface; move in a wave like manner to move
substances along the cell’s surface.

CELL-CELL JUNCTIONS
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 The points where two cells come together. Through the cell junctions, the cells
are joined in long term associations, forming tissues and organs.

Trivia:

People with sickle cell disease have abnormal hemoglobin genes. This causes their red blood
cells to assume a sickle shape. Sickle-shaped red blood cells are not flexible, and thus, they
stick to vessel walls resulting in abnormal blood flow. This then impedes the delivery of
oxygen to the tissues, greatly affecting the health of patients.

MITOCHONDRIA and CHLOROPLASTS

MEMBRANE-BOUND ORGANELLES NON-MEMBRANE-BOUND ORGANELLES

NUCLEUS RIBOSOMES
SMOOTH ER CENTRIOLES
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ROUGH ER CYTOSKELETON
GOLGI APPARATUS
VACUOLES and VESICLES
MITOCHONDRIA
CHLOROPLASTA and other plastids
LYSOSOMES
PERIXOSOMES

ENERGY
- In physics, energy is the property that must be transferred to an object in order to perform
work on, or to heat the object. It can be converted in form, but not created or destroyed.
ADENOSINE TRIPHOSPHATE (ATP)
- It is the major energy currency of the cell that provides the energy for most of the energy-
consuming activities of the cell. The ATP regulates many biochemical pathways.
Mechanism: when the third phosphate group of ATP is removed by hydrolysis, a substantial
amount of free energy is released.
ATP HYDROLYSIS
- ATP hydrolysis is the final link between the energy derived from food or sunlight and useful
work such as muscle contraction, the establishment of electrochemical gradients across
membranes, and biosynthetic processes necessary to maintain life.
- Hundreds of reactions in the cell from metabolic transformations to signaling events are
coupled to the hydrolysis (literally meaning “water loosening”) of ATP by water.
- The reaction ATP + H2O ADP + Pi transforms Adenosine Triphosphate (ATP) into
Adenosine Diphosphate (ADP) and Inorganic Phosphate (Pi).
CHEMICAL REACTIONS:
THE FORWARD ARROW
 When reaction proceeds in forward direction
DOUBLE ARROW
 When reaction is reversible, meaning same products can be used to get the reactant
back
THE EQUILIBRIUM ARROW
 When a reversible reaction is at equilibrium

SYNTHESIS OF ATP

 ADP + Pi ATP + H2O

 Requires energy: 7.3 kcal/mole
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 Occurs in the cytosol by glycolysis

 Occurs in Mitochondria by Cellular Respiration
 Occurs in Chloroplasts by Photosynthesis

CONSUMPTION OF ATP

ATP powers most energy-consuming activities of cells, such as:

 Anabolic (synthesis) reactions such as:

 Joining transfers RNAs to Amino Acids for assembly into Proteins
 Synthesis of Nucleosides Triphosphates for assembly into DNA and RNA
 Synthesis of Polysaccharides
 Synthesis of fats
 Active transport of Molecules and Ions
 Conduction of nerve impulses
 Maintenance of cell volume by osmosis
 Addition of phosphate groups (phosphorylation) to different proteins (e.g., to alter their
activity in cell signaling)
 Muscle contraction
 Beating of cilia and flagella (including sperm)
 Bioluminescence

EXTRACELLULAR ATP

In mammals, ATP also functions outside of cells. ATP is released in the following examples:

 From damaged cells to elicit inflammation and pain

 From the carotid body to signal a shortage of oxygen in the blood
 From taste receptor cells to trigger action potentials in the sensory nerves leading back to
the brain
 From the stretched wall of the urinary bladder to signal when the bladder needs emptying

THE EVOLUTIONARY ORIGINS OF MITOCHONDRIA AND CHLOROPLASTS

 Mitochondria and Chloroplasts display similarities with bacteria that led to the
endosymbiont theory
 This theory states that an early ancestor of eukaryotic cells engulfed an oxygen-using non
photosynthetic prokaryotic cell
 Eventually, the engulfed cell formed a relationship with the host cell in which it was
enclosed, becoming an endosymbiont (a cell living in another cell)
 Indeed, over the course of evolution, the host cell and its endosymbiont merged cells into a
single organism, a eukaryotic cell with a mitochondrion.
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 At least one of these cells may have then taken up a photosynthetic prokaryote, becoming
the ancestor of eukaryotic cells that contain chloroplasts.

EVIDENCES OF THE PAST

 First, rather than being bounded by a single membrane like organelles of the
endomembrane system, mitochondria and typical chloroplast have two membranes
surrounding them. (Chloroplasts also have an internal system of membranous sacs)
 There is evidence that the ancestral engulfed prokaryotes had two outer membranes, which
became the doubled membranes of mitochondria and chloroplasts.
 Second, like prokaryotes, mitochondria and chloroplasts contain ribosomes, as well as
multiple circular DNA molecules associated with their inner membranes.
 Third, also consistent with their probable evolutionary origins as cells, mitochondria and
chloroplast are autonomous (somewhat independent) organelles that grow and reproduce
within the cell.

MITOCHONDRIA (Energy Conversion)

 Singular, mitochondrion
 Mitochondria are the sites as cellular respiration, the metabolic process that uses oxygen to
drive the generation of ATP by extracting energy from sugars, fats, and other fuels.
 The mitochondria are oval shaped organelles found in most eukaryotic cells.
 They are considered to be the powerhouse of the cell.
 As the site of cellular respiration, mitochondria serve to transform molecules such as glucose
into energy molecules known as adenosine triphosphate (ATP).
 ATP fuels cellular processes by breaking its high energy chemical bonds.
 Mitochondria are most plentiful in cells that require significant amounts of energy to
function, such as liver and muscle cells
 Mitochondria are found in nearly all eukaryotic cells, including those of plants, animals,
fungi, and most unicellular eukaryote.
 Some cells have a single large mitochondrion, but more often a cell has hundreds or even
thousands of mitochondria, the number correlatives with the cell level of metabolic activity.
 For example, cells that move or contract have proportionally more mitochondria per volume
than less active cells.
 Each of the two membranes enclosing the mitochondrion is a phospholipid bilayer with a
unique collection of embedded proteins.

The mitochondrion has two membranes that are similar in composition to the cell membrane:

 OUTER MEMBRANE – is a selectively permeable membrane that surrounds the

mitochondria. It is the site of attachment for the respiratory assembly of the electron
transport chain and ATP synthase. It has integral proteins and pores for transporting
molecules just like the cell membrane.
 Fully surrounds the inner membrane, with a small intermembrane space in between.
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 Has many protein-based pores that are big enough to allow the passage of ions and
molecules as large as a small protein
 INNER MEMBRANE – folds inwards (called cristae) to increase surfaces for cellular
metabolism. It contains ribosomes and the DNA of the mitochondria.
 Has restricted permeability like the plasma membrane
 Is loaded with proteins involved in electron transport and ATP synthesis
 Surrounds the mitochondrial matrix, where the citric acid cycle produces the
electrons that travel from one protein complex to the next in the inner membrane.
At the end of this electron transport chain, the final electron acceptor is oxygen, and
this ultimately forms water (H2O). at the same time, the electron transport chain
produces ATP in a process called oxidative phosphorylation.
 The inner membrane creates two enclosed spaces within mitochondria:
 Intermembrane space between the outer membrane and the inner membrane;
and
 Matrix that is enclosed within the inner membrane

CHLOROPLASTS (Capture of Light Energy)

 Chloroplasts, which are found in plants and algae, are the sites of photosynthesis.
 This process converts solar energy to chemical energy by absorbing sunlight and using it to
drive synthesis of organic compounds such as sugars from carbon dioxide and water.
 The word chloroplast is derived from the Greek word chloros which means ‘green’ and
plastes which means ‘the one who forms’
 Chloroplasts are double membrane-bound organelles and are the sites of photosynthesis.
 The chloroplast has a system of three membranes: the outer membrane, inner membrane
and the thylakoid system.

STRUCTURE OF THE CHLOROPLAST

 OUTER MEMBRANE – this is a semi-porous and is permeable to small molecules and ions
which diffuse easily. The outer membrane is not permeable to larger proteins
 INTERMEMBRANE SPACE – this is usually a thin intermembrane space about 10-20
nanometers and is presented between the outer and inner membrane of the chloroplast.
 INNER MEMBRANE – the inner membrane of the chloroplast forms a border to the stroma.
It regulates passage of materials in and out of the chloroplast. In addition to the regulation
activity, fatty acids, lipids, and carotenoids are synthesized in the inner chloroplast
membrane.
 STROMA – this is an alkaline aqueous fluid that is protein-rich and is present within the inne
membrane of the chloroplast. It is the space outside the thylakoid space. The chloroplast
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DNA, chloroplast ribosomes, thylakoid system, starch granules, and other proteins are found
floating around the stroma.
 THYLAKOID SYSTEM – it is suspended in the stroma. It is a collection of membranous
sacks called thylakoids. Thylakoids are small sacks that are interconnected. The
membranes of these thylakoids are the sites for the light reactions of the photosynthesis
to take place. The chlorophyll is found in the thylakoids. The thylakoids are arranged in
stacks known as grana. Each granum contains around 10-20 thylakoids.
 The word thylakoid derives from the Greek word thylakos which means ‘sack’.
 Important protein complexes which carry out the light reaction of photosynthesis
are embedded in the membranes of thylakoids
 The photosystem I and the photosystem II are complexes that harvest light with
chlorophyll and carotenoids. They absorb the light energy and use it to energize the
electrons.
 The molecules present in the thylakoid membrane use the electrons that are
energized to pump hydrogen ions into the thylakoid space. This decreases the pH
and causes it to become acidic in nature.
 A large protein complex known as the ATP synthase controls the concentration
gradient of the hydrogen ions in the thylakoid space to generate ATP energy. The
hydrogen ions flow back into the stroma.

Thylakoid are of two types:

o GRANAL THYLAKOIDS
 Arranged in the grana
 These circular discs that are about 300-600 nanometers in diameter
 Contains only photosystem II protein complex
 This allows them to stack tightly and form many granal layers with granal
membrane
 This structure increases stability and surface area for the capture of light
o STROMAL THYLAKOIDS
 Are in contact with the stroma and are in the form of helicoid sheets
 The Photosystem I and ATP synthase protein complexes are present in the
stroma
 These protein complexes act as spacers between the sheets of stromal
thylakoids

CHLOROPLASTS

 As with mitochondria, the static and rigid appearance of chloroplasts in micrographs or

schematic diagrams is not true to their dynamic behavior in the living cell
 Their shape is changeable, and they grow and originally pinch in two, reproducing
themselves.
 They are mobile, and with mitochondria and other organelles, move around the cell along
tracks of the cytoskeleton
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 The chloroplast is the specialized member of a family of closely related plant organelles
called plastids.
 One type of plastid, the amyloplast, is a colorless organelle that stores starch (amylose)
particularly in roots or tubers.
 Another is the chromoplast, which has pigments that gives fruits and flowers their orange
and yellow hues.

PLASTIDS

 Plastos: folded or molded

 A major double-membrane organelle (cells of plants, algae and some eukaryotic organisms)
 Site of manufacture and storage of important chemical compounds used by the cell.
 Often contain pigments used in photosynthesis, and the types of pigments present can
change or determine the cell’s color

MAJOR PLANT PIGMENTS AND THEIR OCCURRENCE

PIGMENT COMMON TYPES WHERE THEY ARE FOUND EXAMPLES OF

TYPICAL COLORS
Chlorophylls Chlorophyll Green plants Green
Carotenoids Carotenes and Bacteria. Green plants (masked by Oranges, reds,
xanthophylls (e.g. chlorophyll) vegetables like yellows, pinks
astaxanthin) carrots, mangoes and so on. Some
birds, fish and crustaceans absorb
them through their diets

Flavonoids Anthocyanins, aurones, Produce many colors in flowers. Yellow, red, blue,
chalcones, flavonols, and Common in plants such as berries, purple
proanthocyanidins eggplants, and citrus fruits.
Present in certain teas, wine and
chocolate.

Betalains Betacyanins and Flowers and fungi Red to violet, also

betaxanthins yellow to orange