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Before
Introduction to cells, organelles
and biomolecules

After
Cell structure, organelles and
organization of life

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Come to class!!!!!! Try not to fall behind!!

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References Review lecture notes

Read book chapters.
1. Principles of Biochemistry by Lehninger,
Nelson and COX
2. Biochemistry by Lubert Stryer
3. Textbook of Biochemistry with clinical
correlations by Devlin
4. Harper’s Biochemistry- with clinical
correlations
Principles of Biochemistry Principles of Biochemistry
5th Edition 3rd Edition

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Feel Free
Use tools to memorize
to see me!

Histidine? Email for a private

audience
ekanduma@uonbi.ac.ke

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Summary The Cell

¡ An organism is made up of tissues which are divided into tiny
¡ Cells and cell organelles compartments referred to as cells.
l Biochemical structure of animal cell ¡ The cell is the unit of Biological organization
l Structure of cell organelles and their functions ¡ It’s the structural and functional unit of a living organism.
l Structure of bacterial cell ¡ Biochemical reactions take place in the cell.
¡ Organization of life and hierarchy of ¡ Most cells are surrounded by a cell membrane which is
biomolecules selectively permeable.
¡ Within the cell is the cytoplasm in which most catalyzed
¡ Biological membranes, structure and reactions take place.
functions ¡ Cells have a dimension, are relatively small e.g E. coli is 1-
2micrometer.
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Organization and structure of Cells Prokaryotic cell

¡ It’s a single cell of bacteria and primitive algae.
¡ There are two types of cells:-
¡ These are simple and small cells ranging from
¡ Prokaryotic cells
1-2 micrometers.
¡ No nucleus or organelles
¡ They have an outer cell wall and have no
¡ Eukaryotic cells
¡ Much larger in size than prokaryotes
organelles.
¡ 103-104 times larger. ¡ The DNA occurs as the nucleoid.
¡ Has many organelles e.g nucleus, ER, Golgi, ¡ They have flagella for movement and pili for
mitochondria, etc.
attaching on other cells or surfaces.

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Eukaryotic cell

¡ Eukaryotic cells are found in protozoa, plants

and animal cells.
¡ They are highly structured, are large and well
developed.
¡ They are 20-30 um in diameter with a bigger
cell volume.
¡ They have membrane bound compartments in
the cytoplasm referred to as organelles.

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Animal Cell Illustration

The Nucleus

¡ Contains DNA, RNA and is surrounded by a

nuclear envelope which is a double
membrane.
¡ The membrane has openings referred to as
nuclear pores
¡ Nuclear pores are window openings that help
in communication between the nucleus and
the cytoplasm.

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Structure of the nucleus Nucleus

¡ The nucleolus contains RNA and produces

ribosomes involved in protein synthesis in the
cytoplasm.
¡ The rest of the nucleus is chromatin which is mainly
DNA & protein evenly distributed which becomes
organized into discrete granular bodies, the
chromosomes.
¡ The nucleus of eukaryotic cells is very complex both
in its structure and biological activity compared with
that of prokaryotes.

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Mitochondria Mitochondria

¡ Function - site of cellular respiration i.e. the
release of chemical energy from food
¡ Structure - composed of modified double unit
membrane (protein, lipid).
- inner membrane infolded to form cristae
¡ They also contain small amounts of DNA,
RNA and ribosomes.
¡ They vary in number, size, shape and location
depending on the type of the cell
¡ In a liver cell, there are about 1000 copies
¡ Yeast cell and sperm cells contain few but
large mitochondria
¡ The extent of formation of cristae varies with
the type of cell, liver mitochondria have few
cristae while heart cells have numerous

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Structure of the mitochondrion

Endoplasmic Reticulum (ER)
¡ Structure - sheets of unit membrane with ribosomes on
the outside.
¡ Forms a tubular network throughout the cell.
¡ It is a network of sacs that manufactures, processes,
and transports chemical compounds for use inside and
outside of the cell.
¡ Provides a large surface area for the organization of
chemical reactions and synthesis e.g. lipid
biosynthesis.
¡ It is connected to the double-layered nuclear envelope,
providing a pipeline between the nucleus and the
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Golgi apparatus
¡ Function - modifies chemicals to make them
functional e.g. post-translational modification
of proteins.
¡ Structure - stacks of flattened sacs of unit
membrane (cisternae).
¡ Vesicles pinch off the edges.
¡ Secretes chemicals in tiny vesicles e.g.
proteins.
¡ Stores chemicals.

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Functions of Golgi Apparatus

¡ Devoted to processing the proteins synthesized in
the endoplasmic reticulum.
¡ Major processing activity is glycosylation: the
adding of sugar molecules to form glycoproteins.
¡ Cut small peptides, e.g., some hormones and
neurotransmitters, as they traverses the Golgi,
which are too small to be synthesized directly by
ribosomes.

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Lysosomes
¡ Lysosomes are spherical organelles contained
by a single layer membrane found in animal
cells.
¡ The membrane protects the rest of the cell
from the harsh digestive enzymes contained
in the lysosomes.
¡ The cell is further safeguarded from
exposure to the biochemical catalysts present
in lysosomes by their dependency on an
acidic environment.
Lysosomes
¡ Lysosomes contain about 40 different types of
hydrolytic enzymes e.g. esterases, phosphatases,
glucosidases, nucleases, proteinases, lipases,
DNases, RNases etc.
¡ The pH of about 4.8 in the lysosomal matrix
favour enzymatic activity
¡ the neutral environment of the cytosol renders
most of the digestive enzymes inoperative.
¡ Lysosomes are budded from the membrane of the
Golgi apparatus

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Structure of lysosomes Lysosome functions

¡ The main function digestion of cellular

materials that have exceeded their lifetime or
are otherwise no longer useful.
¡ They break cellular waste products, fats,
carbohydrates, proteins, and other
macromolecules into simple compounds
¡ These are then transferred back into the
cytoplasm as new cell-building materials.

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Lysosomes Functions Peroxisomes

¡ Lysosomes found in all animal cells, but most
numerous in disease-fighting cells, such as white ¡ Peroxisomes resembles lysosomes and like them
blood cells. are bound by a single membrane.
¡ These cells involved destruction bacteria, viruses, ¡ They are also filled with enzymes.
and other foreign intruders.
¡ In some cells lysosomes have a secretory function ¡ However, peroxisomes bud off from the
— releasing their contents by exocytosis endoplasmic reticulum- not the Golgi apparatus
¡ Cytotoxic T cells (CTL) secrete perforin from where lysosomes come from.
lysosomes. ¡ The peroxisomal enzymes and other proteins are
¡ Mast cells secrete some of their many mediators of synthesized in the cytosol.
inflammation.
¡ Melanocytes secrete melanin from modified
lysosomes.
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Proteosomes
Functions of Peroxisomes
¡ Breakdown (by oxidation) of excess fatty ¡ Proteosomes are large protein complexes inside all eukaryotes and as
well as in some bacteria.
acids.
¡ In eukaryotes, they are located in the nucleus and the cytoplasm
¡ Breakdown of hydrogen peroxide, a ¡ Its function is to degrade un-needed or damaged proteins by
potentially dangerous product of fatty-acid proteolysis.
oxidation. ¡ Proteosomes are part of a major mechanism by which cells regulate
the concentration of particular proteins and degrade misfolded
¡ It is catalyzed by the enzyme-Catalase- proteins.
present in peroxisomes. ¡ Degradation process yields peptides of about 7-8 amino acids, which
are further degraded into amino acids and used in synthesizing new
¡ Synthesis of cholesterol, lipids and bile acids.
proteins.
¡ Breakdown of excess purines to uric acids. ¡ Proteosomal degradation is essential for many cellular processes, e.g.
cell cycle, regulation of gene expression, and responses to oxidative
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Cell Membrane/Plasma membrane

¡ Cell membrane encloses their contents and serves as a semi-
Cytoplasm porous barrier to the outside environment.
¡ Cytoplasm - Also called protoplasm-where the functions for ¡ The membrane acts as a boundary, holding the cell constituents
cell growth, metabolism, and replication are carried out. together and keeping other substances from entering.
¡ It is a gel-like matrix composed of water, enzymes, nutrients, ¡ It is permeable to specific molecules, however, and allows
wastes, and gases and contains cell structures such as nutrients and other essential elements to enter the cell and waste
ribosomes, mitochondria, ER, Golgi apparatus, lysosomes materials to leave the cell.
etc
¡ All cellular components are scattered throughout the
cytoplasm
¡ The cell envelope encases the cytoplasm and all its
components.

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Viruses
What is a virus?
¡ A tiny particle made up of just genetic material
(DNA or RNA) that can invade and replicate within
a living host.
¡ Viruses are regarded as nonliving chemicals
¡ They do not respire, eat, or excrete.
¡ By itself, a virus cannot do anything.
¡ Viruses can infect bacteria, animal and plant cells
Prions
¡ Are infectious agent that is composed primarily of protein.
¡ Prions propagate by transmitting a mis-folded protein state.
¡ As with viruses a prion itself does not self-replicate, rather it
induces existing polypeptides in the host organism to take on
the rogue form.
¡ The mis-folded form of the prion protein has been implicated in
a number of diseases in a variety of mammals.
¡ Bovine spongiform encephalopathy ("mad cow disease") in
cattle
¡ Creutzfeldt–Jakob disease (CJD) in humans.
¡ Known prion diseases affect the structure of the brain or other
neural tissues.

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Distinctive properties of living systems

Organization of Life
1. Elements ¡ Organisms are complicated and highly organized
2. Simple organic compounds (monomers) ¡ Biological structures serve functional purposes
3. Macromolecules (polymers) ¡ Living systems are actively engaged in energy
4. Supramolecular structures transformations
5. Organelles ¡ Living systems have a remarkable capacity for
self-replication
6. Cells
7. Tissues
8. Organisms

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Elements of Life
Hierarchy of structure of a biological system
¡ Living systems are composed mainly of C,
H, O, N elements (non-metals).

¡ These comprise 99.4% of the elements in

living systems.

¡ The hierarchy of structure of a biological Most abundant, essential for all organisms: C, N, O, P, S, H
system is: Less abundant, essential for all organisms : Na, Mg, K, Ca, Cl
l Atoms à Molecules à Macromolecular Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn
Trace levels, essential for some organisms: V, Cr, Mo, B, Al,
assemblies à Organelles à Cells Ga, Sn, Si, As, Se, I,
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Important compounds, functional groups

Biomolecules-the molecules of life

¡ Biomolecules are chemical compounds that make

up living organisms.
¡ Are complex molecules due to their size and large
structure
¡ Also referred to as macromolecules-which have
different functions.
¡ All macromolecules in the cell are made up
simple, small monomeric units that may be similar
or different in structure and in number.

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Biomolecules: The Molecules of Life

Building Blocks

¡ These small monomeric units are referred to as ¡ What property unites H, O, C and N and
building blocks or precursor molecules e.g renders these atoms so appropriate to the
1. Proteins are made from the 20 standard amino chemistry of life?
acids.
2. DNA is made up nucleotides derived from 4
¡ Answer: Their ability to form covalent bonds
different bases.
by electron-pair sharing.
3. Carbohydrates are made up simples sugars
linked together.

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Main Biomolecules A biomolecular Hierarchy

¡ The main biomolecules are:- ¡ Simple molecules are the units for building
1. Proteins-Structural, catalysis, transport. complex structures in organisms.
2. Carbohydrates- act as a source of energy. l Metabolites and Macromolecules
3. DNA-Stores genetic information. l Organelles
4. Lipids- components of membrane structures, l Membranes
stored energy. l The cell-unit of life

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Properties of biomolecules reflect their fitness to the

living condition
¡ Macromolecules and their building blocks have a
“Sense” or Directionality.

¡ Macromolecules are Informational.

¡ Biomolecules have characteristic 3D architecture

¡ Weak forces maintain biological structure and

determine biomolecular interactions.
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Shape and 3D
structure of Direction of
biomolecules biomolecules

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Direction of biomolecules
Complexity of biomolecules- Contain many
functional groups

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Summary-Functions of cell membranes

1. Supporting and retaining the cytoplasm (inner cell)

Biological membranes 2. Being a selective barrier

Get nutrients in and waste products out.
Non-polar molecules and some small polar molecules can cross.
Most polar compounds must be specifically transported across
the membrane by proteins (Transport).
3. Communication (signaling, via receptors)
• Information flow through the plasma membrane via a membrane
receptor
4. Some membranes have proteins involved enzymatic reactions e.g.
mitochondria
5. Cell to cell Recognition
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Intracellular membranes serve as physical barriers that allow compartmentalization-

Membranes everywhere…

Biological membranes
¡ All biological membranes contain polar lipids, which
make up 20-80 % of the membrane mass depending
on the type of membrane
¡ The rest is protein
¡ The plasma membrane of animal cells contain equal
amounts of lipids and proteins, the inner
mitochondrial membrane contains about 80% protein
and only 20 % lipid
¡ The myelin membranes of the brain contain about
80% lipid and only 20% protein

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Biological membranes Lipids of biological membranes

¡ Natural membranes are very thin, from 6 to 9 nm,
flexible and fluid
¡ They are freely permeable to small non-polar
molecules but are impermeable to electrically
charged ions such as Na+, Cl-, or H+ and to polar
but uncharged molecules such as sugars
¡ Polar molecules are carried across by transport
systems
¡ Lipid-soluble molecules readily pass through the
membrane
¡ The lipid membranes consist of a mixture of
different kinds of polar or amphipathic lipids
¡ Animal cell membranes contain largely
phosphoglycerides with lesser amounts of
sphingolipids
¡ TGs are present in only very minor amnts in
membranes
¡ The outer plasma membrane contain considerable
amnts of cholesterol and cholesterol esters

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Proteins of biological membranes Features of biological membranes

¡ Some of the membrane proteins are enzymes
¡ Others bind and transport polar molecules
across the membrane
¡ Some are loosely attached to the membrane
¡ Others are embedded in the membrane
structure and sometimes extend completely
thro the membrane
¡ All biological membranes have a great deal in
common as regards organization and
composition:
¡ They have an average thickness
¡ They consist mainly of lipids and proteins
¡ They act as a permeability barriers and are
permeable only for selected substances
¡ They have a specific sidedness or asymmetry

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Features of biological membranes Fluid mosaic model

¡ The nature of phospholipids differ between the outer
and the inner layers
¡ The inner layer has P. ethanolamine & P. serine
while the outer layer contains P. choline and
Sphingomyelin
¡ Some transport system function in only one direction
e.g. the Na+/K+ pump of red cells
¡ The outer surface of plasma membranes is rich in
oligosaccharides of glycoproteins and glycolipids
¡ Postulated by S. J. Singer and G. L. Nicolson (1972).
¡ They proposed that the matrix or continuous part of
the membrane structure is a polar lipid bilayer
¡ The bilayer is fluid because the hydrophobic tails of
its polar phospholipids consist of an appropriate
mixture of saturated and unsaturated fatty acids that
is fluid at the normal temperature of the cell
¡ The membrane also contains proteins, cholesterol
and carbohydrates

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Biomembrane composition (a mosaic)-

Structures of cell membranes

¡ A membrane is a mosaic different molecules

of:
l Phospholipid bilayer structure
l Proteins imbedded
l Proteins attached
l Contains cholesterol (some cells) which increases
fluidity
l Glycolipids and Glycoproteins generally on outer
surface of plasma membrane.

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Different kinds of phospholipids-

* Note their asymmetric distribution in the two membrane

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Semipermeability of cell membranes Membranes proteins

¡ Lipid bilayers are referred to as semipermeable because, ¡ A membrane is a mosaic of different proteins
while some substances can readily pass from one side of a
lipid bilayers to the other, others do so only with great embedded and dispersed in the phospholipid
difficulty bilayer
¡ Small and/or hydrophobic substances pass through lipid
bilayers with ease. ¡ These proteins vary in both structure and
¡ Large and/or hydrophilic substances show minimal function
potential for crossing lipid bilayers.
¡ Lipid bilayers tend to be impermeable to such things as ¡ These proteins occur in two arrangements:
proteins, amino acids, nucleic acids, and carbohydrates
¡ Lipid bilayers are permeable to many lipids, lipid-like
substances, and gasses such as molecular oxygen.

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Integral (intrinsic) proteins Peripheral (extrinsic) membrane proteins

¡ Integral proteins are inserted into the membrane.
¡ Their hydrophobic amino acid R gps are surrounded
by hydrophobic FA portions of phospholipids
¡ This makes them interact with the hydrophobic tails
¡ Most integral proteins are enzymes and transport
systems
¡ Transmembrane, with hydrophobic midsections
between hydrophilic ends exposed on both sides of
the membrane.
¡ Peripheral proteins are not embedded but attached to
the membrane's surface. They may be attached to
integral proteins.
¡ Peripheral proteins are attached at the outer or inner
surface. They may also interact with each other.
¡ Protein parts in contact with the aqueous phase are
often glycosylated
¡ They have hydrophilic amino acids R gps on their
surfaces which bind thro electrostatic interactions to the
polar head gps of phospholipids
¡ These proteins can move laterally along the membrane

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Proteins are embedded on membranes via hydrophobic surfaces-

Membrane proteins Hydrophobic tails Transmembrane domains

Structure of an alpha helix
usually 20 amino acids long

Glycolipid anchor

Fatty acid
anchor

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The fluid quality of membranes Cholesterol and the fluidity of membranes

¡ Membranes are held together by hydrophobic ¡ Cholesterol inserts into bilayer membranes
interactions. with its hydroxyl group oriented toward the
¡ Most membrane lipids and some proteins can aqueous phase and its hydrophobic ring
drift laterally within the membrane. system adjacent to fatty acid tails of
phospholipids.
¡ Molecules rarely flip transversely across the
membrane. ¡ The hydroxyl group of cholesterol forms
hydrogen bonds with polar phospholipid head
groups.

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Cholesterol and the fluidity of membranes Membrane carbohydrates

¡ Interaction with the relatively rigid cholesterol ¡ Some occur covalently bonded to lipids
decreases the mobility of hydrocarbon tails of (glycolipids).
phospholipids.
¡ Most covalently bonded to proteins
¡ The presence of cholesterol in a phospholipid
membrane interferes with close packing of fatty acid (glycoproteins).
tails in the crystal state, and thus inhibits transition ¡ They vary from species to species, between
to the crystalline state. individuals of the same species and among
¡ Phospholipid membranes with a high concentration cells in the same individual.
of cholesterol have a fluidity intermediate between
the liquid and crystal states.

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Membrane carbohydrates and cell-cell Membrane carbohydrates and cell-cell

recognition recognition

¡ Cell-cell recognition is the ability of a cell to determine if ¡ Lectins produced by certain plants are specific
other cells it encounters are alike or different from itself proteins capable of binding and agglutinating cells

¡ Cell-cell recognition is crucial in the functioning of an ¡ The do so by binding to carbohydrate moieties on the
organism cell surface e.g. concanavalin A & ricin of the castor
bean
¡ Cells recognize other cells by cell markers found on the
external surface of the cell membrane ¡ Lectins of plants and invertebrates appear to be
defensive since they lack immune cells
¡ Such cell markers are membrane carbohydrates which are
usually branched oligosaccharides
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Structure of a biological membrane

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