THE CELL AND ITS BEGINNINGS ■ One of them able to magnify 270 times

Earliest Microscopic Observations ○ “Animalcules”

● Robert Hooke ■ Little animals
○ Devised of the first microscopes ■ He saw them moving around
○ Most commemorative work came from a thin slice of ■ Now known today as protozoa - single-celled
cork from the bark of an oak tree organisms
○ 2 layers of bark ○ First to observe living cells
■ Inner layer
● Living vascular tissues Contributors to the Cell Theory
○ Xylem (water) ● Matthias Jakob Schleiden
○ Phloem (nutrients) ○ Botanist
■ Outer layer ○ Plants are made up of cells
● Cork ● Theodor Schwann
○ Impermeable buoyant material ○ Physiologist
○ Phellem layer of bark tissue ○ Animals are made up of cells
(protective layer of dead cells) (along with findings of other scientists, they all confirmed that cells are
○ Composed of suberin, a fundamental units of life and that the bodies of living organisms are
hydrophobic substance made up of cells)
● Cork cambium ● Rudolf Carl Virchow
○ Found in vascular plants as part ○ Physician
of the epidermis ○ All cells come from preexisting cells
○ Between cork and primary
phloem The Cell Theory
○ Cellulae ● All organisms are composed of one or more cells
■ From the porous structures he saw ● Cells are the smallest and basic units of structure and function
■ Latin word for “small room” in organisms
■ Reminded him of empty barren rooms where ● Cells arise only from previously existing cells
monks spend most of their time
○ Observations were drawn and recorded in a Cell History
manuscript called Micrographia ● Process
○ The hollow chambers were not living, they were just ○ Protocells - ​self-organized, endogenously ordered,
walls of dead plant cells spherical collection of lipids proposed as a
● Antonie van Leeuwenhoek stepping-stone toward the origin of life
○ Credited to be the first to study magnified cells ○ Living cells
○ Devised his own microscope after getting Micrographia ○ Unicellular
○ Able to devise 500 lenses during his lifetime ○ Multicellular
● Organic chemical evolution
○ The formation of complex organic molecules from
simpler inorganic molecules through chemical
reactions in the oceans during the early history of the
Earth
○ States that the first forms of true living cells have
evolved from protocells from inorganic molecules in
earth’s prebiotic oceans
○ Protocells - formed by the polymerization of organic
molecules in heated rocks or clay
○ Proofs
■ Aleksandr Oparin
● Proposed that organic molecules might
have been assembled in Earth’s
primitive atmosphere in the presence of
strong energy
● Strong energy
○ Heat from volcanoes and
meteorites
○ Radioactivity from the isotopes of
Earth’s crust
○ Electric currents from lightning
○ Ultraviolet radiation from the sun
■ Stanley Miller
● Designed an experiment to test Oparin’s
hypothesis
● Placed a mixture of inorganic
compounds in a closed system
(resembling strong, reducing
atmosphere of the primitive Earth)
● Heated the mixture and then applied an
electric spark
● After a week, amino acids and other
organic compounds were recovered
from the setup
THE INVSBL WORLD THROUGH THE LENS OF A MICROSCOPE
Microscope
● Micrograph
○ image produced by the microscope
○ Specifies the type of microscope used to produce the
image as well as the magnification value of the image
● Magnification
○ Measure of optical instruments for an object to appear
larer than its actual size
○ Example: magnification of 400x means the object
under microscopic study is 400x larger than it’s actual
size
● Resolution
○ Indicates clarity of an image
Types of Microscopes
● Compound microscope
○ Commonly used in schools
○ Equipped with lenses to enlarge objects up to several
hundred times
○ Most powerful magnification: 2000x
○ Used to examine cells and sections of tissues with the
use of sunlight or artificial light to illuminate the object
● Stereomicroscope
○ Used to examine the external structures of a specimen
such as insects
● Phase-contrast microscope
○ Used to examine highly transparent objects such as
unstained cells
● Electron microscope
○ Uses streams of electrons to enlarge objects up to
10,000,000x
○ Transmission electron microscope (TEM)
■ Used to study internal structures of cells
through sectioned specimens
○ Scanning electron microscope (SEM)
 ■ Used to examine the three-dimensional surface
structures or shapes of objects such as viruses
○ Though most electron micrographs are always black
and white, scientists often add artificial colors to allow
certain structures to have enough visibility through the
use of computers
● Fluorescent microscope
○ Illuminates objects stained with fluorescent dyes that
glow in the dark
○ Fluorescent microscopy has been used extensively in
studying the location of certain organelles or
substances inside the cell
● Confocal scanning microscope
○ Used to examine the three-dimensional structure of a
cell or organelle without cutting the specimen into
sections
○ Uses laser beams to scan across the specimen
● Video microscopy
○ Process in which objects examined using the different
microscopes can be photographed or viewed on TV or
computer screens
BASIC CELL TYPES
All living things have cells that share ​fundamental structural parts
● Cell membrane/plasma membrane
○ Outer boundary
○ Regulates the passage of materials into and out of the
cell
● Cytoplasm
○ Gel-like substance which fills the cell’s internal
environment where organelles are suspended in
microscopic fibers (cytoplasm)
● Nucleus
○ Central genetic region where inherited information in
the form of DNA is stored
○ DNA - provides instructions to make proteins, regulate
activities, and enable cells to reproduce
Two main types of cells
1. Prokaryotes
● “Pro” - before; “Karyon” - nut; before the nut
● First kind of cell; 3.5 billion years ago
● Simple organisms possessing cells that are smaller in size
with simpler internal structures
● Examples: bacteria, blue-green algae, archaeans (bacteria
living in extreme conditions)
● Reproduce very fast because of their small size and simple
structure
● Can exist in great numbers in air, water, soil, bodies of living
hosts
● Lack membrane-bound organelles
● Part of a prokaryotic cell
○ Its organization is enclosed by a plasma membrane
encased within a rigid cell wall
■ Plasma membrane
● Phospholipid bilayer
● Semi-permeable membrane
● Responsible for the prokaryote to allow
waste products to pass through while
preventing the diffusion of essential
products to the external environment
■ Cell wall
● Responsible for maintaining shape,
especially when cells are exposed to
high water influx
○ Capsule
■ Acts as a protective layer made up of
polysaccharides (a carbohydrate (e.g. starch,
cellulose, or glycogen) whose molecules
consist of a number of sugar molecules bonded
together) lying outside the cell wall
○ Nucleoid region
■ Lacks distinct nucleus but has nucleoid region
■ Irregularly shaped region where DNA is stored
○ Cytoplasm
■ Not organized into distinct interior
compartments
■ Ribosomes are scattered throughout the
cytoplasm
○ Plasmid
■ Independent circular DNA structure (apart from
its chromosomal DNA)
■ Provides the bacteria with some genetic
advantages (ex. Antibacterial resistance)
○ Appendages that enable cell-to-cell communication
■ Flagellum
● Tail-like appendage
● Allows locomotion
● Whiplike tail moving back and forth - tail
rotates 360 degrees
● Sometimes seen at the end or scattered
randomly over the surface of the cell
■ Fimbriae
● Additional smaller and bristle-like fibers
that grow over the prokaryotic cell’s
surface
■ Conjugation pili
● Tubular structures present in the cell
surface
● Function for cell-to-cell communication
Conjugation Pili
and to pass DNA from one cell to
another
2. Eukaryotes
● Larger in size and has more complex structural components
● Higher forms of organisms: fungi, plants, animals, protists
● Have their own genetic material (DNA) encased within a
distinct nucleus
 ● Have many membrane-bound interior compartments ● Glycerol and phosphate group join together to form the head
● Organelles are neatly arranged of a phospholipid
● Animal and plant cells are eukaryotic ○ Bears a charge so it is considered a polar molecule
○ Polar head can join hydrogen bonds with water
molecules
○ Hydrophilic
● Fatty acids make up the tail
○ Considered nonpolar, cannot form hydrogen bonds
with water
● Nonpolar tails are attracted to each other, face inward where
there is no water
● Polar (hydrophilic) heads face two different directions
○ Facing towards external environment
○ Face the interior cytoplasm
● Properties of the polar heads cause the polar heads and
nonpolar tails to arrange themselves in layers
● Proteins
○ Integral proteins - embedded within the membrane
PARTS OF A CELL ○ Peripheral proteins - found on the surface of the
Cell Structures for Protection membrane
Plasma/cell Membrane
● Thin barrier that forms a boundary, separating an individual
cell from the external environment
● Bag that secures the cell’s contents
● Living system that controls the passage of needed materials
into and out of the cell
○ Gatekeeper
○ Regulates passage of important molecules, oins, and
gases
● Consists of a phospholipid bilayer embedded w/ a variety of
molecules
● Each phospholipid molecule consists of three basic parts
○ Charged phosphate group
○ Glycerol
○ Two fatty acid chains
 ○ Serve as identification tags, enabling cells to
distinguish one type of cell from another
● Membrane proteins
○ Transport proteins
■ extend from phospholipid layer to help materials
cross the membrane
○ Channel proteins
■ form tunnels that help import or export needed
materials and expel waste
○ Cell recognition proteins
■ enable cells to distinguish their own from others
(pathogens)
○ Enzymatic proteins
■ participate in metabolic reactions (degradative
and synthetic reactions)
■ Enzymes - speed up chemical reactions
○ Cytoskeleton proteins
■ Act as muscle and skeleton
■ Maintain cell shape and motility
○ Junction proteins
■ Assist cell-to-cell adhesion and communication
between cells
○ Receptor proteins
■ Antennas or signals for other cells
■ Facilitate exchange of signals with other cells
Other membrane structures by changing shape to allow a specific molecule,
● Cholesterol molecules the ligand, to bing to it
○ Help strengthen the cell membrane
○ Makes it more flexible but less fluid
■ Makes membrane less permeable to
water-soluble substances like ion and simple
sugars
● Carbohydrates
○ Attached to membrane proteins
 ■ Cell membrane is flexible, not rigid
● Phospholipids are able to move side to
side and slide past each other within
each layer
● Membrane behaves like fluid
● Can break but eventually reassemble
(from a video)
● Proteins that are embedded in the
membrane stay in their specific areas
■ Variety of molecules scattered along the
membrane provides variety of different textures
and patterns making up a mosaic
Cell Wall
● Only present in plant cells, algae, fungi, and bacteria
● Surrounds cell membrane, additional boundary to it
● Rigid layer that gives protection, rigid support, and shape to
the cell
● Cell walls of multiple cells can cling to each other to support an
entire organism
● Cell wall’s composition varies, related to different needs of
each type of organism
○ Plants and algae - polysaccharide cellulose
■ Have openings or channels to let water and
● Uniqueness of cell is governed by unique molecular markers other molecules diffuse
embedded in their matrix and make it possible for other cells to ○ Fungi - chitin
be recognized and interact with ○ Bacteria - peptidoglycan
○ Allows cell-to-cell communications
○ Paves way for them to form tissues or organs
● Fluid mosaic model
○ describes the structure of the plasma membrane as a
mosaic​ of components —including phospholipids,
cholesterol, proteins, and carbohydrates—that gives
the membrane a ​fluid​ character
○ Mosaic - image produced when arranging small pieces
together
○ 2 descriptions
 ● Cytosol
● Liquid portion consisting mainly of water and excluding the
organelles in it
○ Chemical makeup - high concentration of water
■ Suggests it’s necessary for maintaining cell
structure
■ Water - essential component of life
■ Many chemical reactions occur in the cytoplasm
where water acts as a natural solvent

Genetic Control Organelles

Nucleus
● Storehouse of genetic information in the form of DNA
● Directs all activities of the cell following strictly the instructions
in DNA
● Protects DNA at all times from damage, instructions must be
made available for use at proper times
○ There are molecules that could damage DNA, which is
why it has to be kept safe in the nucleus
● DNA
○ Long chain of molecule
○ Can be segmented into portions called genes (contain
instructions for making proteins
○ Packaged by a special group of protein - Histones,
forming a complex structure - Chromatin
○ Chromatin further condenses to form tightly coiled
structure - Chromosome
● Nuclear Envelope
○ Special membrane that encloses the DNA
○ Filled with holes - Nuclear pores - allow large
molecules to pass between the nucleus and cytoplasm
● Nucleolus
○ Dense region where small organelles (ribosomes)
Cytoplasm essential for making proteins are assembled
● Fills the space between the nucleus and the cell membrane ■ Ribosomes are formed in the nucleus
● Cytosol

Manufacturing, Storage, Distribution, Breakdown Organelles
Endoplasmic Reticulum
● Interconnected network of thin and folded membranes
● Fills much of the large portion of the cytoplasm
● Composition is similar to nuclear membrane and cell
membrane
● Lumen - Interior of the maze
○ Site for many processes such as the production of
proteins and lipids
● Rough ER
○ Surface of the ER covered by ribosomes
○ Dotted with ribosomes that join amino acids together to
form proteins
○ Looks bumpy under a microscope
○ As proteins are being made in the ribosomes, they
enter the lumen where proteins are modified further
with the addition of sugar chains adding to stability
○ Proteins on Er - usually either incorporated into the cell
membrane or secreted to areas where my body needs
them
● Some ribosomes are not bound in ER and used chemical
reactions within the cell
● Smooth Endoplasmic Reticulum
○ Not studded with ribosomes
○ Responsible for the production of lipids and
performance of offer specialized functions (ex.
Breaking down alcohol)
Golgi Apparatus
● From the ER, proteins are transported here
● Layered stacks of membrane-enclosed spaces
● Where proteins are processed, sorted, and delivered
● Have enzymes that further modify the proteins
● Finished products are also packaged here
○ Some of the packaged proteins are temporarily stored
within the Golgi Apparatus for later use
○ Some are transported to other organelles within the cell
or carried to the membrane where they will be secreted
out of the cell
 ● Cisface - receive ● New vesicles at the end of the Golgi Apparatus are formed for
● Cisternae - package storage, transport, or secretion
● Transfase - transform ● Vesicles have various functions
○ Storage vesicles
○ Transport vesicles
○ Secretory vesicles
● Vesicles are generally short-lived and are formed and recycled
as needed
● Synthesis, storage, and export of molecules is made possible
because organelles are functionally connected to each other
○ Instruction from nucleus from nuclear pore to ER
○ Transport vesicles from ER to Golgi Apparatus
○ Vesicles from GA to other destinations
● Some vesicles may develop into lysosomes and vacuoles

Vacuoles
● fluid -filled sac for the storage of materials needed by the cell
○ Includes water, food molecules, inorganic ions, and
enzymes
● Most animal cells contain many small vacuoles
● Plant cells have a central vacuole
○ Single large vacuole that takes up most of the space
inside a plant cell
○ Most of the time dislodges the nucleus to the side
○ Filled with a water fluid that strengthens the cell and
Vesicles helps support the entire plant by making it erect
● Organelles are connected to each other ○ Plants wilt because there’s not enough water in the
○ By means of membranes central vacuole
○ By the transfer of materials through vesicles ○ May also contain other substances
● Small, membrane-bound sacs ■ Toxins that can harm predators
● After a protein is manufactures, part of the ER pinches off to ■ Waste products that can harm itself
form vesicles ■ Pigments that give colors to the petals
○ Protein is protected and is transferred to the Golgi
Apparatus where further modifications are made
 Peroxisomes
● Also exist as small vesicles around the cell
● Surrounded by a single membrane containing digestive
enzymes for breaking down toxic material
● Carry out oxidative enzymes that require oxygen
● Absorb nutrients that had been acquired by cells
● Enzymes in peroxisome break down complex molecules into
smaller molecules
● By product of digestion - hydrogen peroxide (H2O2)
○ Catalase in peroxisomes destroys it by breaking it
down into water and oxygen
■ Water is safe for the cell na
■ Oxygen is needed for the digestive reaction that
follows
● Also help breaking down alcohol in the body
● Liver cells have more peroxisomes than other cells in the body

Lysosomes
● Round-shaped, membrane-bound structures containing
chemicals that can break down materials in the cell
● Contain powerful enzymes (lysozyme) which defend a cell
from invading bacteria and viruses
● Break down damaged or worn-out cell parts
● More numerous in animal cells than in plant cells

Energy-Processing Organelles
Mitochondria
● Supply energy to the cell
● Bean-shaped and have two membranes
○ Inner membrane - has many folds that greatly increase
its surface area
 ○ Here, a series of chemical reactions converters ■ Light-absorbing pigment that gives plants their
molecules from the food you eat into usable energy green color
● Have their own ribosomes and DNA ■ Plays a role in photosynthesis
○ Suggests that they were originally free-living ○ Organized into stacks
prokaryotes that were taken in by larger cells ● Granum
● Crista junction - folds of the inner membrane ○ A stack of thylakoids
● Intermembrane space - space between ● Stroma
● Matrix - fluids ○ Liquid portion of the chloroplast
● Lamellae
○ connects
● Have their own ribosomes and DNA
● Present in plant cells
○ Work together with mitochondria to capture and
convert energy
● Also found in algae

Plastids
● Chloroplasts are organelles that help a plant convert solar
energy to chemical energy
○ Carry out photosynthesis - series of complex chemical
reactions that transform solar energy to energy-rich
molecules that the cell can use
● Highly compartmentalized like the mitochondria Structural Support, Movement, and Communication between cells
● Have inner and outer membrane Centrosome and Centriole
● Thylakoids ● Centrosome
○ Sacs ○ Small dense region of the cytoplasm
○ In the membrane ○ Serves as the main microtubule organizing center
○ Contain chlorophyll (MTOC) where microtubules are assembled
 ○ In animal cells
■ Contains two barrel-like structures called
Centrioles that are perpendicular to each other
■ Centrioles - cylinder shaped organelles made of
nine trplets of short microtubules arranged in a
ring
● Before animal cells divide, centrosome and centrioles double
○ Two new centrosomes move to the opposite ends of
the cell
● Microtubules develop from each centrosome, forming spindle
fibers
○ Affix to chromatids and help divide them between two
cells
● Centrioles - organize microtubules to form cilia and flagella

Cilia and Flagella

● Two locomotory projections in eukaryotes
● Allow cell to move like an oar or a whip
● Same structural composition
○ Contain 9 microtubule doublets called 9+2 pattern
● Cilia
○ Look like little hairs with much shorter length
○ Move in coordinated fashion
○ Like motion of oars in a rowing team
● Flagella
○ Look like a whip or a tail
● Movement of cilia and flagella result in swimming
● For cells anchored in tissue - ciliary motion sweeps liquids
across cell surface

Cytoskeletons
● There is a protective membrane capable of receiving
messages from other cells
● Internal environment filled with membrane-bound organelles
● Membrane bound organelles are anchored to specific sites in
the cell interior
● Removing the cell membrane will not cause the cell to collapse
of ooze out its content
● Cytoskeleton - flexible network of framework
○ Made up of a small protein subunit
○ Forming long threads of fibers that can crisscross the
entire cell
○ Provides sturdy mechanical balance
○ Help the cell to organize its contents and to direct the
cell’s movement in response to the cell’s changing
needs and signals from its external environment
● 3 flexible networks of protein
○ Microtubules
■ Lengthy and thickes
■ Stiff, hollow tubes
■ Give the cell shape
 ■ Serve as ​anchorage​ for the membrane-bound
organelles and other cell parts
■ Act as “tracks” for the movement of vesicles
and other cell components
■ During cell division, they​ form spindle fibers
■ Form permanent structures (like the flagellum)
○ Intermediate filaments
■ Smaller than microtubules
■ Ropelike in appearance
■ Give the cell ​tensile strength​/the ability to
stretch without breaking apart
■ Prominently present in skin cells/other part
subject to mechanical stress
■ Important in ensuring the strength or claws,
hairs, and feathers of animals
○ Microfilaments
■ Thinnest
■ Actin filaments
■ Tiny, flexible filaments
■ Provide protective meshwork under the plasma
membrane
■ Important in cell movement, ​allow muscles to
contract and relax
● Animals have complex cell surface, possess several types of
junctions
○ Tight junctions - join two cells tightly together to form a
leak proof sheet
○ Adhesion junctions - act like screws with cytoskeletal
fibers to form strong sheets
○ Gap junctions - similar to plasmodesmata; allow small
molecules to flow between neighboring cells
● Extracellular mix
○ Layer mix of proteins and polysaccharides
(glycoproteins) secreted from tissue cells
○ Act as a glue to bind the cells together in tissues and
provide mechanical strength
○ Enables cells to communicate with surrounding cells to
signal development, movement, and coordination
within a tissue sheet

Cell Surfaces and Junctions

● Tissues - collection of cells that carry out a specific function
○ Individual cells must interact with neighboring cells
○ When they interact, they lay side-by-side/pressing
directly against each other
● All cells are joined together by junctions
● Plants
○ Adjacent cells function in a coordinated way by
communicating through numerous channels called
plasmodesmata
○ Plays an important role in the sharing of water,
nutrients, and chemical messages among plants