Chapter 2

Protoplasm:
o Cytoplasm: extends from the plasma membrane to the nuclear envelop
o Karyoplasm: the substance forming the contents of the nucleus

Cytosol: water in which inorganic and organic chemicals are dissolved. The fluid that
fills the cytoplasm. Contains organelles
Organelles: are metabolically active cellular structures that execute specific
functions.
Cell membrane: forms a selectively permeable barrier between the cytoplasm and
the external milieu. Functions:
o Maintaining the structural integrity of the cell
o Controlling movements of substances in and out of the cell (selective
permeability)
o Regulating cell-cell interactions
o Recognizing, via receptors, antigens and foreign cells as well as altered cells
o Acting as an interface between the cytoplasm and the external milieu
o Establishing transport systems for specific molecules
o Transducing extracellular physical or chemical signals into intracellular
events.
In the electron microscope the plasma membrane appears as a trilaminar structure.
The plasmalemma is composed of a phospholipid bilayer and associated integral and
peripheral proteins.
Each leaflet is composed of a single layer of phospholipids and associated proteins,
usually in a 1:1 proportion by weight. In certain cases, such as myelin sheaths,
however, the lipid component outweighs the protein component by a ratio of 4:1
Phospholipid: Phospholipid molecule is amphipathic.
o polar head (hydrophilic): composed of glycerol, to which a positively charged
nitrogenous group is attached.
o two nonpolar (hydrophobic) fatty acid tails. Only one of which is usually
saturated
The bond between the two fatty acid tails which are facing each other is weal non
covalent bond.
The unsaturated fatty acyl molecules increase membrane fluidity, whereas cholesterol
decreases it (although cholesterol concentrations much lower than normal increase
membrane fluidity).
Membrane proteins:
o Integral proteins: are dissolved in the lipid bilayer. They are also referred to
as transmembrane proteins because they span the entire thickness of the
plasma membrane.
o Peripheral proteins: do not extend into the lipid bilayer, these proteins are
located on the cytoplasmic as well as the extracellular space.
o Multipass proteins: transmembrane proteins that are folded, they pass back
and forth across the plasmalemma,

o Membrane transport proteins: are two types, channel proteins and carrier
proteins, they facilitate the movement of aqueous molecules and ions across
the plasmalemma.

Fluid mosaic model: the ability of protein to float like icebergs in the sea of
phospholipids.
P-face: The outer surface of the inner leaflet (closer to the protoplasm)
E-face: The inner surface of the outer leaflet (closer to the extracellular space)
Glycocalyx: composed usually of carbohydrate chains, coats the cell surface. Most
important function is protection of the cell from interaction with inappropriate
proteins, from chemical injury and from physical injury.
A few nonpolar molecules (e.g., benzene, oxygen, nitrogen) and uncharged polar
molecules (e.g., water, glycerol) can move across the cell membrane by simple
diffusion down their concentration gradients.
Passive transport: transport of molecules across the plasma membrane down a
concentration gradient.
o Simple diffusion: transports small nonpolar molecules and small, uncharged
polar molecules.
o Facilitated diffusion: occurs via ion channels and/or carrier proteins. Faster
than simple diffusion
Active transport: is an energy-requiring process that transports a molecule against an
electrochemical gradient via carrier proteins.

Channel proteins may be gated or ungated; they are incapable of transporting

substances against a concentration gradient.

Gated channels:
o Voltage-gated channels: these channels go from the closed to the open
position, permitting the passage of ions from one side of the membrane to the
other. Some of these channels have a refractory period where the channel is in
inactive position.
o Ligand-gated channels: channels that require the binding of a ligand
(signaling molecule) to the channel protein to open their gate. Includes
neurotransmitter-gated channels and nucleotide-gated channels
o Mechanically-gated channels: an actual physical manipulation is required to
open the gate.
o G-protein-gated ion channels: certain gated ion channels require the
interaction between a receptor molecule and a G-protein complex with the
resultant activation of the G protein. The activated G protein then interacts
with the channel protein, modulating the ability of the channel to open or
close.

Ungated channels:
o Potassium (K+) leak channel, which permits the movement of K+ across it
and its instrumental in the creation of an electrical potential difference
between the two sides of the cell membrane
o Aquaporins: Multipass proteins that form channels designed for the passage
of water from one side of the cell membrane to the other. Aquaporins is
completely impermeable to protons.
o Carrier proteins: are multipass transmembrane proteins that undergo
reversible conformational changes to transport specific molecules across the
membrane; these proteins function in both passive transport and active
transport

Primary active transport by the NA+-K+ pump: normally the concentration of Na+
is much greater outside the cell than inside, and the concentration of K+ is much
greater inside the cell than outside. Two binding sites for K+ on its extracellular
aspect and three binding sites for Na+ on its cytoplasmic aspect; thus, for every two
K+ ions conveyed into the cell, three Na+ ions are transported out of the cell.

Secondary active transport by coupled carrier proteins

There is no direct coupling of ATP; instead it relies upon the electrochemical potential
difference created by pumping ions in/out of the cell

Cell signaling: is the communication that occurs when signaling cells release
signaling molecules that bind to cell surface receptors of target cells.
1. Lipid-soluble signaling molecules penetrate the plasma membrane and bind to
receptors within the cytoplasm or inside the nucleus, activating intracellular
messengers. Examples include hormones that influence gene transcription.
2. Hydrophilic signaling molecules bind to and activate cell-surface receptors and
have diverse physiologic effects. Examples include neurotransmitters and
numerous hormones (e.g., serotonin, insulin).

Enzyme-linked receptors: These receptors are transmembrane proteins whose

extracellular regions act as receptors for specific ligands. When a signaling molecule
binds to the receptor site, the receptors intracellular domain becomes activated so that
it now possesses enzymatic capabilities

G-proteinlinked receptors: transmembrane proteins associated with an ion channel

or with an enzyme that is bound to the cytoplasmic surface of the cell membrane:
there are several types of G proteins, including:
o Stimulatory (Gs)
o Inhibitory (Gi)
o Pertussis toxin-sensitive (G0)
o Pertussis toxin-insensitive (GBq)

o Transducin (Gt)

Protein synthesis

Ribosomes: They function as a surface for the synthesis of proteins.

o small particles approx. 12 nm wide and 25 nm long.
o Composed of proteins and ribosomal RNA (rRNA).
o They function as a surface for the synthesis of proteins.
o Each ribosome is composed of a large subunit and small subunit.
o Small subunit: 40S (sedimentation value). Composed of 33 proteins and an
18S rRNA. The small subunit has a site for binding mRNA, a P- site for
binding peptidyl transfer ribonucleic acid (tRNA), an A-site for binding
aminoacyl tRNA, and an E-site where the tRNA that gave up its amino acid
exits the ribosome
o Large subunit: 60S. consists of 49 s and 3 rRNA.
o The sedimentation values of the RNAs are 5S, 5.8S, and 28S.
o Ribozymes: rRNA of large subunit which have enzymatic activity and
catalyze peptide bond formation.

Endoplasmic Reticulum: largest membranous system of the cell, participates in the

synthesis of all proteins that are to be packaged or delivered to the plasma
membrane. It also performs post-translational modifications of these proteins,
including sulfation, folding and glycosylation. Lipids and integral proteins of all
membranes of the cell are manufactured by the RER
o Smooth endoplasmic reticulum: it functions in sequestering calcium ions
from the cytosol, assisting in the control of muscle contraction
o Rough Endoplasmic Reticulum: The membranes of this organelle possesses
integral proteins that function in recognizing and binding ribosomes to its
cytosolic surface and also maintains the flattened morphology of the RER
- Integral proteins:
1. Signal recognition particle receptor (docking protein)
2. Ribosome receptor protein (ribophorin I and ribophorin II)
3. Pore protein
o Polyribosomes: is a complex of a mRNA molecule and two or more
ribosomes that is formed during active translation

Messenger RNA: Formed in the nucleus. It carries the genetic code from the nucleus
to the cytoplasm to act as template for protein synthesis. mRNA consists of a series of
codons corresponding to particular amino acids. It also contains a start codon (AUG)
and one or more stop codons (UAA, UAG, or UGA).
o Transcription: begins with attachment of RNA polymerase II to a core
promoter, a specific DNA sequence located next to a gene.

o RNA polymerase II initiates transcription by unwinding the double helix of

the DNA two turns exposing the nucleotides and, therefore, the codons on the
DNA strand.
o The primary transcript is a long, single-stranded RNA molecule, called
precursor messenger RNA (pre-mRNA). It contains both coding segments
(exons) and noncoding segments (introns).
Transfer RNA: Ferries activated amino acids to the ribosome/mRNA complex,
resulting in the formation of the protein. tRNA is a small RNA molecule produced
from DNA by RNA polymerase III. Two regions:
o Anticodon
o The amino acid-bearing region
Ribosomal RNA: forms associations with proteins and enzymes in the nucleus to
form ribosomes. Is synthesized in the fibrillar region of the nucleolus by RNA
polymerase I.

Protein synthesis (translation): occurs on ribosomes in the cytosol or the surface of

the rough endoplasmic reticulum.
o Requirements for protein synthesis:
An mRNA strand
tRNA, each of which carries an amino acid and possesses the
anticodon that recognizes the codon of the mRNA coding for that
particular amino acid
small and large ribosomal subunits
o Protein synthesis process:
1. The process begins when the P-site of the small ribosomal subunit
is occupied by an initiator tRNA whose anticodon recognizes the
triplet codon AUG
An mRNA binds to the small subunits
The small subunit assists the anticodon of the tRNA molecule to
recognize the start codon AUG on the mRNA molecule.
2. The large ribosomal subunit binds to the small subunit and the
ribosome moves along the mRNA chain, until the next codon
lines up with the A- site of the small subunit.
3. An acylated tRNA (tRNA bearing an amino acid) compares its
anticodon with the codon of the mRNA; if they match, the tRNA
binds to the A-site.
4. The amino acids at the A-site and the P-site form a peptide bond.
The tRNA on the P-site yields its amino acid to the tRNA at the Asite, which now has two amino acids attached to it. These reactions
are catalyzed by the rRNA-based enzyme of the large subunit
known as peptidyl transferase.
5. The deaminated tRNA leaves the P-site and binds to the E-site;
the tRNA with its two amino acids attached moves from the A-site
to the P-site
6. When the A-site of the small ribosomal subunit reaches a stop
codon, a release factor binds to the A-site.

Golgi apparatus: functions in the synthesis of carbohydrates and in the

modification and sorting of proteins manufactured on the RER. Golgi apparatus has
slightly curved membrane-bounded cisternae, Golgi stack:
o The cis-face: is closest to the RER, convex in shape. Newly formed proteins
from RER enter the cis-face.
o The medial face (intermediate face)
o The trans-face: concave in shape, considered to be the exit face, the modified
protein is ready to be packaged and to be sent to its destination from here.
o ERGIC (endoplasmic reticulum/Golgi intermediate compartment): is a
collection of vesicles and tubules formed from the fusion of transfer vesicles
derived from the final cisterna of the RER, known as transitional
endoplasmic reticulum (TER)
o Golgi- and Rough endoplasmic endothelium associated vesicles: Vesicles
associated with the RER and Golgi apparatus possess a protein coat as well as
surface markers.
Coatomer I (COP I)
Coatomer II (COP II)
Clathrin
o Vesicles leaving the ER COP II
o Vesicles to the cis-face
o Vesicles to the trans-face
o Vesicles to the trans Golgi network

COP I

o Vesicles that arise from the trans Golgi network require the presence of
clathrin for their formation.
o Retrograde transport: vesicles transporting proteins from the cis end of the
Golgi complex back to the rough endoplasmic reticulum (ER), where they
were originally synthesized, and between Golgi compartments. (COP I)
o Anterograde transport: COP II
o The MTOC is located near the Golgi complex. The end of the microtubule
near the Golgi is called minus end.
o Sorting in the Trans Golgi network: the trans Golgi network is responsible for
the sorting of proteins to their respective pathways so that they reach the
plasma membrane, secretory granules, or lysosomes. Cargo that leaves the
TGN is enclosed in vesicles that may do one of the following:

Insert into the cell membrane as membrane proteins and lipids

(exocytosis)
Fuse with the cell membrane such that the protein they carry is
immediately released into the extracellular space (exocytosis)

Congregate (gather) in the cytoplasm near the apical cell membrane

as secretory granules (vesicles), and, upon a given signal, fuse with
the cell membrane for eventual release of the protein outside the cell.
(exocytosis)
Fuse with late endosomes, releasing their content into that
organelle, which then becomes a lysosome

Endocytosis, endosomes and lysosomes are involved in the ingestion, sequestering,

degradation of substances internalized from the extracellular space.

Endocytosis:
o Phagocytosis: if the vesicle is large (>250 nm in diameter), the method is
called phagocytosis (cell eating). The vesicle is a phagosome. The cells are
called phagocytes. The most common phagocytes are the white blood cells,
the neutrophils, and the monocytes. Macrophages and neutrophils possess
Fc receptors that bind the Fc regions of the antibody upon contact.
o Membrane trafficking: the movement of membranes to and from various
compartments of the cell. Cells must maintain their shape and size and
therefor they remove excess membrane and return it for recycling.
o Pinocytosis: if the vesicle is small (<150 nm in diameter), the type of
endocytosis is called pinocytosis (cell drinking) and the vesicle is a
pinocytotic vesicle. A typical pinocytotic vesicle may have as many as 1000
cargo receptors.

Receptor-mediated endocytosis:

Cargo receptors: are transmembrane proteins that become

associated with the particular macromolecule (ligand)
extracellularly and with a clathrin coat intracellularly

Dynamin: a GTPase that help releasing the pinocytotic vesicle

is from its membrane origin. It surrounds the constricted neck
of the vesicle, pinch its neck closed, and the vesicle is released
from its membrane origin into the cytoplasm

Endosomes: are divided into two compartments: early endosomes, near the
periphery of the cell, and late endosomes, situated deeper within the cytoplasm. The
membrane of all endosomes contain ATP- linked H+ pumps.
o Early endosomes: a system of vesicles and tubules located near the plasma
membrane. Has a pH of 6.0
o Late endosomes: a system of vesicles and tubules located deeper in the
cytoplasm near the Golgi apparatus, helps to prepare its contents for eventual
destruction by lysosomes. Has a pH of 5.5
o Transcytosis: occurs as membrane-bound carriers selectively transport
materials between one part of the cell and another in order to maintain
unique environments on either side of the cell

Lysosomes: have an acidic pH and contain hydrolytic enzymes. The contents of late
endosomes are delivered for enzymatic digestion into the lysosomes. Lysosome
membrane possess proton pumps that actively transport H+ ion into the lysosome
maintaining the pH-level at 5.0, because the enzymes in the lysosomes require an
acid environment.
o Substances reach the the lysosomes in one of three ways:

Phagosomes: moves toward the interior of the cell. The enzymes

digest most of the contents of the phagosome, especially the protein
and carbohydrate components. Lipids, are more resistant to complete
digestion and remain enclosed within the spent lysosome, now referred
to as residual body.

Autophagosomes: senescent (old) organelles such as mitochondria

and organelles no longer required by the cell, or the RER need to be
degraded. They become surrounded by elements of the endoplasmic
reticulum and are enclosed in vesicles called autophagosomes

Pinocytotic vesicles

Peroxisomes: are self-replicating organelles that contain oxidative enzymes.

Peroxisomes contain enzymes that use molecular oxygen to oxidize various substrates
and break them down into smaller components
o The highly toxic hydrogen peroxide H2O2 is generated by these oxidations
and then becomes converted into water and oxygene by one of peroxisomal
enzymes catalase
Proteasomes: are small organelles composed of protein complexes that are
responsible for proteolysis of malformed and ubiquitin-tagged proteins.
Mitochondria possess their own DNA and perform oxidative phosphorylation
(produce ATP) and lipid synthesis.
Smooth outer membrane
Folded inner membrane
Intermembrane space: the narrow area between inner and outer membrane.
Matrix space: large space enclosed by the inner membrane.
The inner membrane is folded into cristae to provide a larger surface for ATP
synthase.
o Oxidative Phosphorylation: the process responsible for the formation of
ATP.
o Inclusions: nonliving components of the cell that do not possess metabolic
activity and are not bounded by membranes
Glycogen
o
o
o
o
o

 Lipids
o Pigments: most common is the hemoglobin of the red blood cells.
Next most common is melanin:
Skin and hair
Cells of the retina
Specialized nerve cells of substantia nigra