ORGANIZATION AND STRUCTURE OF CELLS:

A cell is the basic structural and functional unit of an organism OR A cell is the basic unit of life

A cell is able to perform essential vital functions such as metabolism, growth, movement,
reproduction, and hereditary transmission ,Growth, reproduction, and hereditary transmission
can be achieved by cell division.

There are two primary types of cells: eukaryotic cells and prokaryotic cells. Eukaryotic cells
are called so because they have a true nucleus. The nucleus, which houses DNA, is contained
within a membrane and separated from other cellular structures. Prokaryotic cells however have
no true nucleus. DNA in a prokaryotic cell is not separated from the rest of the cell but coiled up
in a region called the nucleoid.
PROKARYOTIC AND EUKARYOTIC ORGANISMS

All forms of life are composed of only two fundamentally different types of cells.Prokaryotic,
Pro meaning Before and Karyon meaning Nucleus, these the ancient/old/first form of cells to
exist, examples of organisms with these types of cell include: bacteria and archeans

Eukaryotic, Eu meaning true and Karyon Nucleus, these evolved from prokaryotes and are recent
cells, they are found in bodies of, plants, animals, and protist. The most important feature of this
type of cell is presence of membrane bound organelles.

Difference between the Eukaryotic and prokaryotic cell

Prokaryotic cell Eukaryotic cell

Unicellular Muilticellular

Single membrane with rigid cell wall Lipid bilayer membrane with proteins

No well defined nucleus Nucleus well defined

Cytoplasm without cell organelles Membrane bound with cell organelles present

Cell division by fission, Cell division by mitosis

RNA and protein synthesis occur in the RNA synthesis and processing in the nucleus.
nucleus or same compartments Proteins synthesized in the cytoplasm

Mitochondria absent Mitochondria is the power house

Lysosome absent Lysosome present

Cytoskeleton absent Cytoskeleton present

Golgi apparatus abscent. Polysaccharide Golgi apparatus present

granule storage

Example: bacteria,cynobacteria, Example:fungi,plants,animal cell

FUNCTION OF CELL PARTS

Chromosomes

- Usually in the form of chromatin

- Contains genetic information
- Composed of DNA
- Thicken for cellular division
- Set number per species (i.e. 23 pairs for human)

Nuclear membrane

- Surrounds nucleus
- Composed of two layers
- Numerous openings for nuclear traffic

Function.

 The external membrane is continuous with the membrane of

the endoplasmic reticulum (ER).
 The mRNA exported from the nucleus travels to the
ribosomes , which either float freely in the cytosol or are
 bound to the cytosolic side of the endoplasmic reticulum.
 Each ribosome is made up of proteins associated with a
number of structural RNA molecules called ribosomal RNA
(rRNA).
 Ribosome assembles the genes and enter biochemical
“machinery” for protein synthesis (translation).

Nucleus and nucleolus

- Spherical shape
- Visible when cell is not dividing
- Contains RNA for protein manufacture

Function.

Contains a liquid known as karyolymph, a nucleolus, and chromatin.

Chromatin contains deoxyribonucleic acids (DNA), the carriers of

genetic information.

Site for the synthesis of DNA and RNA and Protein through the
process of DNA replication, Transcription, Translation.

Site for the post transcription modification like splicing, 5’ capping

and polyadenylation.

Nuclear pores:

- Are high-molecular-weight protein complexes (125 MDa) located

within the nuclear envelope.

Function.

They allow large molecules such as transcription factors, RNA

polymerases or cytoplasmic steroid hormone receptors to pass into
the nucleus, nuclear molecules such as mRNA and tRNA to pass out
of the nucleus, and other molecules such as ribosomal proteins to
 travel both ways and The reaction is (ATP-dependent).

Centrioles

- Paired cylindrical organelles near nucleus

- Composed of nine tubes, each with three tubules
- Involved in cellular division
- Lie at right angles to each other

Chloroplasts

- A plastid usually found in plant cells

- Contain green chlorophyll where photosynthesis takes place

Cytoskeleton

- Composed of microtubules
- Supports cell and provides shape
- Aids movement of materials in and out of cells

Function:

Allows the cell to maintain and change its shape (during cell division,
etc.), make selective movements (migration, cilia), and conduct
intracellular transport activities (vesicle, mitosis).

It contains actin filaments as well as microtubules and intermediate

filaments (e.g., vimentin and desmin filaments, neurofilaments, keratin
filaments) that extend from the centrosome.
Endoplasmic reticulum

- Tubular network fused to nuclear membrane

- Goes through cytoplasm onto cell membrane
- Stores, separates, and serves as cell's transport system
- Smooth type: lacks ribosomes
- Rough type (pictured): ribosomes embedded in surface

Function of endoplasmic reticulum:

The ER membrane containing the synthesized membrane proteins or

export proteins forms vesicles which are transported to the Golgi
apparatus.

 rough endoplasmic reticulum- Ribosomes can attach to the

cytosolic surface of parts of the ER, forming a rough
endoplasmic reticulum (RER).These ribosome synthesize export
proteins as well as transmembrane proteins for the plasma
membrane, endoplasmic reticulum, Golgi apparatus, lysosomes,
etc.
 smooth endoplasmic reticulum-Contains no ribosomes and is the
production site of lipids (e.g., for lipoproteins.) and other
substance

Golgi apparatus

- Protein 'packaging plant' and modification

- A membrane structure found near nucleus
- Composed of numerous layers forming a sac

Function.

 Polysaccharide synthesis; protein processing (post translational

modification), e.g., glycosylation of membrane proteins.
 packaging” of proteins meant for export into secretory vesicles
 (secretory granules), for example, the contents of which are
exocytosis into the extracellular space,

Lysosome

- Digestive 'plant' for proteins, lipids, and carbohydrates

- Transports undigested material to cell membrane for removal
- Vary in shape depending on process being carried out
- Cell breaks down if lysosome explodes

Mitochondria

- Second largest organelle with unique genetic structure

- Double-layered outer membrane with inner folds called cristae
- Energy-producing chemical reactions take place on cristae
- Controls level of water and other materials in cell
- Recycles and decomposes proteins, fats, and carbohydrates, and forms
urea.

Function:

site of oxidation of carbohydrates and lipids to CO2and H2O and

associated O2 expenditure. The Krebs cycle (citric acid cycle), respiratory
chain and related ATP synthesis also occur in mitochondria.

Ribosomes

- Each cell contains thousands

- Miniature 'protein factories'
- Composes 25% of cell's mass
- Stationary type: embedded in rough endoplasmic reticulum
- Mobile type: injects proteins directly into cytoplasm

Function:
Machinery for protein synthesis

Vacuoles

- Membrane-bound sacs for storage, digestion, and waste removal

- Contains water solution
- Contractile vacuoles for water removal (in unicellular organisms)

Cell wall

- Most commonly found in plant cells

- Controls turgity
- Extracellular structure surrounding plasma membrane
- Primary cell wall: extremely elastic
- Secondary cell wall: forms around primary cell wall after growth is
complete

Peroxisomes.

Are microbodies containing enzymes (imported via a signal sequence)

that permit the oxidation of certain organic molecules (R-H), such as
amino acids and fatty acids: R-H22+ O2R + H2O.

The peroxisomes also contain catalase, which transforms 2 H2O2 into

O2+ H2O and oxidizes toxins, such as alcohol and other substances.

Plasma membrane

- Outer membrane of cell that controls cellular traffic

- Contains proteins (left, gray) that span through the membrane and allow
passage of materials
- Proteins are surrounded by a phospholipids bi-layer.
 Function:

 The phospholipids mainly consist of

phosphatidylcholine ,phosphatidylserine,
phosphatidylethanolamine, and sphingomyelin.
 The hydrophobic components of the membrane face each other,
whereas the hydrophilic components face the watery
surroundings, that is, the extracellular fluid or cytosol.
 The lipid composition of the two layers of the membrane differs
greatly. Glycolipids are present only in the external layer,
Cholesterol (present in both layers) reduces both the fluidity of the
membrane and its permeability to polar substances.
LIPID BILAYER (PLASMA MEMBRANE):

Chemical composition of membranes:

The membrane are made up of 40% of lipids, 10% of carbohydrates and 40% of proteins.
The carbohydrates are covalently bound to the proteins or lipids
The lipids are the structural components of cell membrane. It contains both the ionic polar
(Hydrophilic) head and non-polar (hydrophobic) tail.
Types of lipids present at the membranes:
1. FATTY ACIDS
Long chain in nature and they are major components and make up the non-polar ends of the
lipids and attached to polar end of glycerol.
50% are saturated fatty acids( no double bond) i.e palmitic acids(16 C atoms),stearic acids(18 C
atoms) and the remaining 50% is made up of both unsaturated and poly unsaturated fatty acids
i.e oleic acids most abundant in animal membranes cells. Others include arachidonic acids(20 C
atoms), linoleic acids (18C atoms), linolenic acids (18 C atoms). The degree of unsaturation
depends on the fluidity of the membranes
2. GLYCEROPHOSPHOLIPIDS:
These are the compound lipids that are present in the lipid membranes. These include

 Phophstidyl ethanol amine (cephalin)

  Phosphatidyl choline (lecithin)
 Phosphatidyl serine
3. SPHINGOLIPIDS:
These are the lipids that are found on the membrane of a tissue of the nervous system. They
include;
 Sphingomylin
 Cerebrosides
 Gangliosides 60% of grey matter cells of the brain
4. CHOLESTEROL:
It is found in the eukaryotic cells and it helps in the regulation of the fluidity of the animal
membranes

FLUID MOSAIC MODEL OF A MEMBRANE:

The fluid mosaic model structure was proposed by J.S.Singer and G.L. Nicholson in the year
1972
According to J.S.Singer and G.L. Nicholson suggestion, the biological membranes are
composed of proteins and phospholipids and the model is believed that the phospholipids
bilayer is fluid matrix and a solvent to proteins. Both the lipids and proteins are capable of
rational and lateral movements.
The proteins are associated with the surface of this lipid bilayer or are embedded in the bilayer to
varying degrees.
The model defined two types of membrane proteins:

 Intrinsic(integral ) proteins
 Peripheral (extrinsic)proteins
Intrinsic (integral) proteins are deeply embedded and the peripheral proteins are loosely attached.
The membrane proteins, hence this will make them to float on top environment of fluid
phospholids bilayers. This is similar to icebergs floating in the sea water. The integral proteins
are responsible for the Lateral diffusion as well as Transverse movements. The lipids also have
the transverse movement from one face of the bilayer to the other ( flip-flopping)
Mechanism of transport in a typical membrane:

The lipophilic cell membrane protects the cell interior from the extracellular fluid, which has a
completely different composition.
This is imperative for the creation and maintenance of a cell’s internal environment by means of
metabolic energy expenditure.
Channels (pores), carriers, ion pumps and the process of cytosis allow transmembrane
transport of selected substances including the import and export of metabolic substrates and
metabolites and the selective transport of ions used to create or modify the cell potential , which
plays an essential role in excitability of nerve and muscle cells, and exchange of some materials
like carbon dioxide and water molecules hence allowing the cell to maintain the pH and the
undesirable change in cell volume.
Due to presence of different compartments of organelles, there are different mechanisms of
transport.
Nuclear pores in the nuclear envelope provide the channels for RNA export out of the nucleus
and protein import into it;
Protein transport from the rough endoplasmic reticulum to the Golgi complex ;
Axonal transport in the nerve fibers, in which distances of up to 1 meter can be crossed .
These transport processes mainly take place along the filaments of the cytoskeleton.
INTRACELLULAR TRANSMEMBRANE TRANSPORT
Main sites:
1. Lysosomes:
Uptake of H+ ions from the cytosol and release of metabolites such as amino acids into the
cytosol
2. Endoplasmic reticulum (ER):
In addition to a translocator protein , the ER has two other proteins that transport Ca2+
Calcium can be pumped from the cytosol into the ER by a Ca2+-ATPase called SERCA
(sarcoplasmic endoplasmic reticulum Ca2+-transporting ATPase). The resulting Ca2+stores can be
released into the cytosol via a Ca2+channel in response to a triggering signal.
3. Mitochondria:
The outer membrane contains large pores called porins that render it permeable to small
molecules (5 kDa), and the inner membrane has high concentrations of specific carriers and
enzymes . Enzyme complexes of the respiratory chain transfer electrons (e–) from high to low
energy levels, thereby pumping H+ions from the matrix space into the inter-membrane space ,
resulting in the formation of an H ion gradient directed into the matrix. In addition to driving
ATP synthetase (ATP production), but also promotes the inflow of pyruvate and an organic
phosphate, Pi –(symport; ). Ca2+ions that regulate Ca sensitive mitochondrial enzymes in
muscle tissue can be pumped into the matrix space with ATP expenditure, thereby allowing the
mitochondria to form a sort of Ca2+buffer space for protection against dangerously high
concentrations of Ca2+in the cytosol.

TRANSPORT OF MACROMOLECULES:

The macromolecules that can be transported include proteins, hormones, immunoglobulin,

lipoprotein (LDL) and even in viruses.
The dependant mechanisms include:
A. Exocytosis
B. Endocytosis
Exocytosis:
 Also referred to as reverse of pinocytosis
 Is the process of release of macromolecules to the exterior by cells
 Example: membrane remodeling when the components are synthesized in the Golgi
apparatus are carried in a vesicle to the plasma membrane by the cytoplasmic contractile
element in the macro-tubular system hence externalization.

Categories of exocytosised macromolecules:

1. They can attach to the cell surface and become peripheral proteins i.e antigens
2. They can within become part of the extracellular matrix e.g collagen and
glycosaminoglycans (GAGs)
3. Hormones like insulin, parathohormone (PTH) and catecholamine are all packed in
granules, processed within cell to be released upon appropriate stimuli.
Endocytosis.
This is the process through which the cells ingest parts of their plasma membranes.
1. The endocytic vesicles are formed when segment of plasma invaginates enclosing a
minute volume of extracellular fluid(ECF) and its contents hence pinches off as fusion of
plasma membranes seal the neck of the original site of invagination.
2. The vesicle fuses then joins or fuses with other membrane structures and transports its
contents to other cellular compartments. The endocytic vesicles fuses with primary
lysosomes to form secondary lysosomes which contains hydrolytic enzymes hence
specialized organelles for intracellular disposal
Factors required for the endocytosis:
 Energy: usually derived from ATP hydrolysis
 Calcium ions
 Contractile elements in the cell-probably the microfilaments system
Types of endocytosis:
Endocytosis
Phagocytosis Pinocytosis

Fluid phase pinocytosis receptor mediated

absorptive pinocytosis
PHAGOCYTOSIS:
This is the engulfment of large particles like viruses, bacteria, cells, or debris of macrophages
and the granulocytes
It involves the biochemical mechanism known as “respiratory burst” in which oxygen
consumption is increased and leads to formation of super oxide ion (O2¯)
 The engulfed large particle extend pseudopodia and surround the particles to form ”
phagosomes’’
 Phagosomes fuses with the Lysosome to form “phagolysosomes’’ in which the particle is
digested
PINOCYTOSIS:

This is the property of a cell and leads to the cellular uptake of fluids and fluid contents.

1. Fluid phase pinocytosis:

This is a nonselective process of a solute by formation of small vesicles which is
proportionate to its concentration in extracellular fluid (ECF)
2. Receptor mediated absorptive pinocytosis:
 The eukaryotic cell have a structure like coated vesicles and endosomes that are involved
in the transport of macromolecules from the exterior to the interior of the cell.
The external surface of the plasma membrane are covered with receptors and coat pits.
The cell surface are rich in receptor proteins that combine with macromolecules(ligands)
The membrane bound receptors proteins move literally into coat pits
These coats pits are rapidly pinched off and are internalized as coated vesicles
The peripheral protein “clathrin’’ combine with the coated vesicles and get hydrolysed
by the protein “dynamin’’ a GTP hence pinching off from the cell surface
Example: low density lipoprotein (LDL) molecules bound to receptors are internalized by
means of coated pits

TRANSPORT MECHANISM:
The following are the mechanism of transport across the bio-membranes:
 Passive diffusion or simple diffusion
 Facilitated diffusion
 Active transport
A. Passive diffusion: or simple diffusion:
The movement of solute from a region of higher concentration to region of lower concentration
through a semi permeable membrane till the equilibrium is attained
It requires neither energy nor protein carrier. And it operates UNIDIRECTIONALLY.
Example of molecule that are transported are: water, gases, pentose sugars
Factors affecting the diffusion process:
Concentration gradient-the solutes move from higher concentration to a lower concentration
Electrical potential-solutes move to the direction that has different charges usually inside the cell
it is negatively charged
Hydrostatic pressure gradient-increase in pressure increases the rate of collision between the
molecules
Temperature-increase in temperature increases the particle motion and increases the frequency
of collision between external particles and the membrane
Permeability coefficient-net diffusion depends on the permeability coefficient for the membrane

B. Facilitated diffusion:
Movement of molecule from higher concentration to a lower concentration (along the
concentration gradient) with the help of a carrier of transport protein. There is no energy is
required and can operate bidirectional.
This occur in the transport and the absorption in the ping pong model.
Example: Absorption of Fructose in the intestine

C. Active transport:
This is the movement of molecule from a lower concentration to a higher concentration (against
the concentration and the electrical gradient) with the utilization of energy, requires carrier or a
specific protein transporter.

Chemistry of biomolecules:

CHROMATOGRAPHY

 Most forms of chromatography use a 2-phase system to separate substances on the basis
of some physical-chemical property.
 One phase is usually a stationary phase. The second phase is usually a mobile phase
(often a buffer in biochemistry) that carries the sample components along at different
rates of mobility.
 The separation is based on how well the stationary phase retards the components versus
how quickly the mobile phase moves them along.
  Substances with different properties will thus elute (exit) from the column at different
times.
 Some common types of column chromatography used in biochemistry are gel filtration,
ion exchange, and affinity.
 You will have the opportunity to use one or more of these during your projects. In this
exercise, you will use gel filtration chromatography.
(a) Gel Filtration (permeation) Chromatography.
 Gel filtration uses a gel matrix as the stationary phase.
 The matrix consists of very small porous beads. The large molecules of a sample solution
do not get “caught” in the pores of the gel and will travel through the column more
rapidly because they can go around the beads.
 They are said to be “excluded” from the matrix. Smaller molecules that can enter the gel
pores must go through the beads, thus taking more time to reach the bottom of the
column.
 Medium-size molecules can enter larger pores, but not small ones.
 This form is also referred to as “molecular sieve” chromatography, because the
components of a sample are separated according to their molecular size (and to a certain
extent, molecular shape).
 The gel matrices are commonly made of cross linked polysaccharides or polyacrylamide,
both of which can be made with varying pore sizes.
 The information supplied by the manufacturer will state the size of the beads, the
approximate size of molecules that will be excluded, and the range of molecular weight
range that can be separated.
 By using gels of different sizes and porosities, one can separate samples that have a large
variety of components.


Affinity Chromatography.
 Affinity chromatography utilizes the specific interaction between one kind of solute
molecule and a second molecule that is immobilized on a stationary phase.
 For example, the immobilized molecule may be an antibody to some specific protein.
 When solute containing a mixture of proteins is passed by this molecule, only the
specific protein reacts to this antibody, binding it to the stationary phase.
 This protein is later eluted by changing the ionic strength or pH. Alternatively, an excess
of the molecule immobilized on the stationary phase may be used.
 For example, if the molecule you wish to purify binds glucose, it can be separated from
molecules that don’t by using a glucose affinity column (the matrix contains immobilized
glucose molecules).
  Only glucose-binding molecules will bind to this matrix.
 The bound molecules can be eluted by adding glucose to the elution buffer. This will
compete with the matrix-bound glucose for the binding sites on the protein and the
proteins (now bound to free glucose) will dissociate from the matrix and elute from the
column.
 This method is gentler, but can only be used in some cases. This elution method is only
feasible when the immobilized molecule is small, readily available, and cheap, as is the
case with glucose.
NB.

Covers these areas;

Paper chromatography, affinity chromatography, gel elution chromatography, gas

liquid chromatography, high performance liquid chromatography (HPLC), thin layer
chromatography, quantitative and qualitative procedures applied in different Methods
of separation of chemical compounds in chromatography .
Those areas where notes are not there you can make some and include.