The Cell Cytoplasm

Objectives
• General
 Get general idea of cell organization.
 Understand what changes in organelles tell you about dynamics of cells.
 Develop global perspective on cell function
• Specific (as in the learning objectives)

The Cell Cytoplasm: Outline:

I.Introduction
II. Plasma membranes
III. Organelles
IV. Cytoskeleton
V. Inclusions

Introduction
• Subunits if Life:
• Cells are the structural units of all living organisms.
• There are two fundamentally different types of cells
– Prokaryotes
– Eukaryotes

Prokaryotic cells
• Simplest organisms; single cell organisms (bacteria)
– Cytoplasm is surrounded by plasma membrane and encased in a rigid cell wall.
• single circular molecule of DNA
• No distinct interior compartments
• No histones (specific proteins bound to DNA)
• No membranous organelles

Eukaryotic cells
• Characterized by compartmentalization by an endomembrane system, and the
presence of membrane-bound organelles.
– Distinct nucleus and envelope
– Chromosomes - DNA associated with protein
– Numerous membranous organelles
– Cytoskeleton (internal protein scaffolding)

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Importance of Studying Cell Structure:
• Changes in cell structure provide:
– important clues about changes in cell function.
– important clues about pathologic changes.
• In pathologic conditions cells exhibit either too much or not enough of a normal
function
Changes in structure can indicate a great deal about what functional changes are
occurring
Liver

Cell Components

• Cytoplasm
– a matrix, or cytosol, in which are embedded the organelles, the cytoskeleton, and
deposits of carbohydrates, lipids, and pigments.
– Plasma membrane encloses the cell- phospholipid bilayer
• The Nucleus
– Houses the genetic material (DNA)

Plasma Membrane
Plasma Membrane: Molecular Composition

Phospholipid Bilayer
– Each phospholipids has a polar head located at surface of membrane(hydrophilic)
– Nonpolar tail of 2 long fatty acid chains (hydrophobic)
– Phospholipids (eg, lecithin, phosphotidylserine, phosphotydylcholine,
phosphotidylethanolamine, sphingomyelin) are by far the most abundant.

• Membrane phospholipids are arranged in a bilayer with their tails directed

toward one another at the center of the membrane
Phospholipids are Asymmetrically Distributed
Phosphatidylcholine and Sphingomyelin more abundant in outer leaflet
Phosphatidylserine, Phosphatidylethanolamine preferentially on inner leaflet

Cholesterol is also a constituent of the membrane and determines the fluidity and help
improve the rigidity.

Proteins
• 50% of membrane weight
• 2 groups
• Integral proteins- span the entire lipid bilayer
• Some trans membrane proteins may serve as hydrophilic channels for the passage
of water and water-soluble materials

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Proteins
• Peripheral proteins- looser connection, usually cytoplasmic, often associated
with 2° messenger system or cytoskeletal apparatus

• Carbohydrates are covalently attached to proteins exposed to the extra cellular

side of the membrane
• glycoproteins and glycolipids

Glycocalyx
• Carbohydrate chains that are covalently linked to integral proteins or
phospholipids
• Composition varies from cell to cell
• Form fuzzy coat on surface of cell
– Added measure of protection to cells
– Bind to substances outside of cell (adhesion)
– Cell recognition

Membrane Structure
Fluid mosaic model of membrane structure
• Fluid mosaic model describes biologic membranes as "protein icebergs in a lipid
sea."
• The mosaic disposition of membrane proteins, in conjunction with the fluid nature
of the lipid bilayer, constitutes the basis of the fluid mosaic model for membrane
structure
• The model is not static.
• Integral proteins exhibit lateral mobility in the bilayer and may undergo
rearrangement determined by their association with peripheral proteins.

Plasma Membrane: Functions

• Maintain structural integrity
• Regulate permeability
• Mediate cell-cell interactions
• Recognize outside environment
• Regulate transport of material in and out
• Transduce signals

Plasma Membrane: Functions

Selective permeability
• Membranes display selective permeability, essential to maintaining the functional
steady state required for cell survival.
• Three mechanisms allow passage of selected molecules.
– Passive diffusion

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– Facilitated diffusion
– Active transport

• Passive diffusion. Certain substances cross the membrane in either direction,

following a concentration gradient. No energy expenditure required.
• Facilitated diffusion. Certain molecules e.g, glucose) must be helped across the
membrane by a membrane component. Follows concentration gradient. No energy
required.
• Active transport.
• Some non diffusible molecules can move into or out of a cell either along or
against a concentration gradient.
• Such movement requires energy, usually as ATP.
• An example of this active transport is the sodium pump (Na +, K+, and Ca +)

Signal Reception
• Many cells form communicating junctions that couple adjacent cells, allowing the
exchange of ions and small molecules
• Through these channels, also called gap junctions, signals pass directly from cell
to cell without reaching the extracellular fluid
• In other cases, cells display membrane-bound signaling molecules that influence
other cells in direct physical contact

Endocytosis
• Cells engulf extracellular substances and bring them into the cytoplasm in
membrane-limited vesicles by mechanisms described collectively as endocytosis.
• Obtain raw materials for cell functions
• Defend organism from noxious chemicals and harmful biologicals

• Phagocytosis
• Macropinocytosis
• Pinocytosis
• Can involve specific receptors on surface or can be passive
• Receptors concentrate uptake
• In all cases some extracellular material internalized passively

Endocytosis

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• In phagocytosis ("cell eating"), the cell engulfs insoluble substances, such as
large macromolecules or entire bacteria. The vesicles formed are termed phagosomes,
• Can involve specific receptors on surface or can be passive
• In all cases some extracellular material internalized passively
• Plasma membrane invaginates to form pit
• Opening of pit constricts to form narrow neck
• Apposing membranes fuse to seal pit into vesicle
• In pinocytosis ("cell drinking"), the cell engulfs small amounts of fluid, which
may contain a variety of solutes.
• Pinocytotic vesicles are usually smaller than phagosomes.
• The pinch off from cell surface and most eventually fuse with lysosomes

• In receptor-mediated endocytosis, the cell engulfs foreign substances along with

their own surface receptors (wide or concentrated in regions called “coated pits”..
• Binding of ligand to receptor induces the collection of ligand receptor complexes
in coated pits, shallow membrane depressions with clathrin protein coats lining their
cytoplasmic surfaces.
• Invagination and pinching off of the pit creates a coated vesicle, which carries the
ligand-receptor complexes into the cell
• The coated vesicles soon lose their clathrin coating and fuse with an endosome,
and the ligands dissociate from the receptors.
• The later “endosomal compartment”, or CURL (compartment of uncoupling of
receptor and ligand), divides into 2 portions, segregating the receptors from the ligands.
• The receptors are returned to the plasma membrane to participate in the formation
of new coated pits.

Exocytosis
• Exocytosis removes substances from the cell.
• Cells use this process both for secretion and for excretion of undigested material.
• A membrane-limited vesicle or secretory granule fuses with the plasma membrane
and releases its contents into the extracellular space, without disrupting the plasma
membrane. (Membrane trafficking).

Organelles

• Cytoplasmic structures comprise 3 groups.

– Organelles: "very small" organs; subcellular constituents with specialized
functions
– The cytoskeleton is a proteinaceous supporting network within the cytoplasm
– Cytoplasmic inclusions are structures, membrane-bound or not, that are
generally more transient than organelles and less actively involved in cell metabolism
leg, lipid droplets).

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Membrane Limited Organelles

Mitochondria
• Membranous bag of proteins involved in aerobic energy production and storage
• Regulate ion content of cytoplasm.
• Store factors important in regulated cell death (apoptosis)
• Vary in size, shape and number
• 0.5 - 1 micrometer in diameter & up to 10 micrometers long
• Move freely within cytosol and tend to aggregate in areas with high energy
demands
• Visible by light Microscopy
• Outer membrane:
– permeable
– contains porin, a transmembrane pore-forming protein which allows free passage
of small molecules
– contains enzymes that convert lipids into forms that can be metabolized by
mitochondria

• Inner membrane:
– separated from outer by “intermembranous space:
– thinner and thrown into folds -- cristae
– highly selective permeability via elementary particles that generates proton
gradient that produces heat and generates ATP via oxidative phosphorylation (aerobic
respiration)

• Inner Matrix:
– rich in proteins and nucleic acids
– Contains enzymes for Krebs cycle, fatty acid beta oxidation and protein
synthesis, mitochondrial DNA, RNA and ribosomes
– contains dense granules which are the storage site for divalent cations
– contains one or more strands of double stranded circular DNA

• Inner Matrix DNA

– Maternally derived
– Produces only a small portion of the protein in mitochondria, rest come via
nuclear DNA transcription of RNA and protein synthesis in cytosolic polyribosomes.
– Imported proteins have a mitochondrial targeting sequence.

• Cells with higher energy demands have more mitochondria and more cristae per
mitochondria

Ribosomes
• Small particles composed of ribosomal RNA and protein
– RNA imparts an intense basophilia to the cytoplasm
• Composition and appearance: beads on a string at the EM level,

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• Beads have a large and small subunit that don’t combine until protein synthesis
begins
• Cytoplasmic basophilia in LM is clue of extensive rER
• Seen as basophilic bodies, Nissl substance in neurons, ergastoplasm in glandular
cells

• Function:
• protein synthesis in either the cytosol (when as free polyribosomes) or as bound
polyribosomes on the endoplasmic reticulum (rough ER)
• -free polyribosomes synthesize intracellular proteins
• -bound (rER) polyribosomes synthesize proteins destined for the extracellular
space or within the membrane - they see extracellular space
Ribosomes & Protein Synthesis

Endoplasmic Reticulum
• Membrane bounded element containing enzymes, receptors, and transporters
• Appears as elongated, flattened, rounded or tubular vesicles that have either a
rough (rER) or smooth (sER) surface with gradations between the two (smooth and rough
ER can share the same lumen)

Rough Endoplasmic Reticulum

• rER consists of interconnecting network of membrane-limited flattened sacs
(cisternae)
• Exterior surface is studded with ribosomes
– 15-20nm in diameter
– contain RNA and protein
– may form groups and be attached to mRNA
• rER is continuous with the outer membrane of the nuclear envelope
• Rough ER is involved in:
– protein synthesis and initial post-translational modification (glycosylation,
sulfation, phosphorylation, and hydroxylation of proteins) for export.
– synthesis of phospholipids
• Extensive rER is evidence of intense protein synthesis (cells specialized for
protein secretion).
– pancreatic acinar cells (digestive enzymes),
– fibroblasts (collagen),
– plasma cells (immunoglobulins).

Smooth Endoplasmic Reticulum

• Short anastomosing tubules that are NOT associated with ribosomes
• When present in large amounts, imparts a distinct acidophilia to the cytoplasm
• Well developed in cells that synthesis and secrete steroids
• Referred to as “sarcoplasmic reticulum” in skeletal and cardiac muscle
– segregates Ca++ essential for contraction

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• SER functions in :
• Steroid synthesis
• Neutralization of poison
• Lipid metabolism
• Phospholipid synthesis
• Glycogen utilization

Golgi Apparatus
• smooth, membrane delimited organelle containing various enzymes
• By EM, stacks of flattened membranes that are closely associated with vesicles .
• 3 components:
– slightly curved flattened stacks (3 - 10) of cisternae
– cisternae nearest to rER is called the forming, convex, or cis face.
– On the opposite side of the Golgi complex, is the maturing, concave, or trans
face,
• several small vesicles near on cis face are transport vesicles
• fewer larger vesicles near the trans face are the condensing vesicles

Golgi Apparatus: Functions

• Continued post-translational modification of proteins includes:
– terminal glycosylation, sulfation, phosphorylation, and limited proteolysis
• Golgi also synthesizes proteoglycans (extensively glycosylated proteins)
• Condensing vacuoles bud from the Golgi cisternae, generating vesicles that will
transport proteins to various sites
• Protein sorting and intracellular addressing: some stay in the ER/Golgi, some to
lyosomes , others into secretory vesicles and yet still some incorporated into cell
membrane.
• Secretory cells usually have more extensive Golgi complexes
Golgi Compartmentalization allows sequential processing
• By LM, clear area partially surrounded by ergastoplasm in cells with extensive
Golgi

Lysosomes
• Lysosomes - membrane-bound vesicles containing a large variety of hydrolytic
enzymes; mostly hydrolases.
• Are a product of the Golgi and fuses with late endosomes to facilitate degradation
of endosome contents
• Are usually spherical, range in diameter from 0.05 to 0.5 micrometer
• In EM present a uniformly granular, electron-dense appearance
• Lysosomes are intracytoplasmic acidic vesicles involved in degradation of
numerous substances
• Lysosomes are particularly abundant in cells exhibiting phagocytic activity
– macrophages,
– neutrophilic leukocytes).

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• Lysosomal enzymes have optimal activity at an acidic pH.

Stages of Lysosomes
• Primary lysosomes have not entered into a digestive event .
• When primary lysosomes fuse with the membrane of the phagosome and empty
their hydrolytic enzymes into the vacuole, the composite structure is now termed a
secondary lysosome.
• After digestion of the contents of the secondary lysosome , indigestible
compounds are retained within the vacuoles, which are now called residual bodies
• When primary lysosomes fuse with an organelle or cell component, the resuling
structure is called autophagosome.

Peroxisomes (Microbodies)
• Small, membrane-limited enzyme-containing vesicles spherical bodies
– 0.5 to 1.0 um in diameter somewhat larger than primary lysosomes
– contain oxidative enzymes -- catalase
• Involved in the formation and breakdown of intracellular hydrogen peroxide
– used for killing phagocytosed bacteria
• Involved in beta oxidation of fatty acids
• Content is moderately electron-dense
.
Secretory Vesicles, or Granules

• Secretory vesicles are membrane structures found in those cells that store a
product until its release
• They contain a concentrated form of the secretory product .
• Secretory vesicles containing digestive enzymes are referred to as zymogen
granules.
Non-membrane Limited Organelles

Cytoskeleton
• Intracellular Movement
– Contraction can move cytoplasm
– Attach to other organelles and with molecular motors coordinate their movement
• Outside-In signalling
– Bind to integral membrane proteins and transduce signals from outside
environment

The Cytoskeleton
• Network of protein fibers that provide:
• Support to cell shape and anchoring organelles
• Support to transport molecules/vesicles within the cell.

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• Intercellular connections linking cells together and attaches to substrate (non-
cellular linkage) linking cell to substrate
• Can be very dynamic

Components of the Cytoskeleton

• Microtubules
• Filaments
– Microfilaments
– Intermediate Filaments
• Microtrabecular components

Microfilaments
• Types
– Thick (13-16 nm diameter) Filaments- Myosin
– Thin (6-8 nm diameter) Filaments- Actin
• Major protein of muscle cells where they are critical component of contraction
apparatus
• Actin (and probably myosin) found in almost all cell types

Actin Microfilaments
• 2 strings of bead-like subunits twisted together in a rope
– globular subunits are stabilized by Ca++ and ATP
– form stable subunits with myosin

Microvilli
• cyclindrical, membrane-bound cytoplasmic projections
• core of 25-30 actin microfilaments crosslinked by villin anchored into terminal
web
– complex of actin and spectrin molecules
Stereocilia
• Long microvilli
• Found only in:
– epididymis
– sensory hair cells of cochlea -- signal generation
• non-motile, rigid structures
• core made of actin filaments

Intermediate Filaments
• Reasonably stable elements serving primarily structural function
• Bind other cytoskeletal and intracellular structures to one another

Microtubules

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• Elongated macromolecules made up of globular protein subunits (hollow
cylinder)
– Composed of heterodimer of alpha tubulin and beta tubulin subunits in helix that
polymerizes into a microtubule
• Polymerization directed by microtuble organizing centers:
– Cilia
– Basal bodies
– Centrosome
• Polymerization can be highly dynamic (mitotic spindle) or can be relatively stable
(cilia)
• Change in length accomplished by fast growth at one end (+) while other end
grows slowly (-) or disassembly at negative end.
• Change in length controlled by environment and MAPs. ( microtubule-associated
proteins)

Microtubule Functions
• Cell shape maintenance and intracellular movement (microtubles are stiff)
• Maintenance of cell polarity
• Chromosome movement during division
• Beating of cilia and flagella
• Track for microtubule-based motor proteins that distribute vesicles throughout the
cell

Centrioles
• Small cylindrical paired structures located in centrosome
• Made of nine sets of microtubule triplets arranged in a circle and linked laterally
forming a centriole
• Each triplet consists of 1 complete and 2 incomplete microtubules fused
• Two centrioles (at 90 degrees) are found near the nucleus of interphase
• In dividing cells, the centrioles duplicate during the S period, migrate to the
opposite poles of the cell and form the organizing centers for the mitotic spindles

Cilia and Flagella

• Are motile processes, covered by cell membrane, with a highly organized
microtubule core.
• Ciliated cells typically possess a large number of cilia.
• Flagellated cells have only one flagellum, with a length close to 100 um.
• In humans, the spermatozoa are the only cell type with a flagellum.
• The main function of cilia is to sweep fluid from the surface of cell sheets.
• Both cilia and flagella possess the same core organization.

Cilia and Flagella

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• Short, fine, hair-like, beating structures
• Associated with basal bodies
– thin, dark-staining band at base of cilia
– Similar to centriole
– result of centriole replication

Cilia
• Contain an organized core of microtubules
– 9 + 2 arrangement
– Contains a pair of dynein arms which make a temporary bridge with the B
microtubule of adjacent doublet
• Abundant in respiratory epithelium, intestine, urogenital tracts
• Beating of cilia moves fluid along surface of sheets of cells
• Abnormal Cilia may be found in chronic respiratory problems

Non-cytoskeletal Contents of Cytosol

Inclusions

• Cytoplasmic deposits are usually transitory components of the cytoplasm,

composed mainly of accumulated metabolites or other substances
• These may result from either normal physiology or pathology
• The accumulated molecules occur in several forms.

Glycogen
• Carbohydrates are stored as glycogen granules
– By LM, stain acidophilic (associated protein) or by carbohydrate stains (PAS)
– by EM, appear as electron-dense particles

Lipids
• Lipids (another storage form for energy)
– stored primarily by adipocytes
– ability to accumulate in other cells
• hepatocytes
– exist as free cytoplasmic droplets

• Pigments
– exogenous such as carotene or dust
– endogenous: produced by the cells
• hemoglobin
• melanin
• lipofuscin -- wear and tear end product

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