There Are Three Distinct Domains of Life

1. Prokaryotes
2. Eukaryotes
3. Archaeabacteria

 Prokaryotes
 These are organisms that do not contain a true nucleus. These organisms also do
not contain organelles such as mitochondria, endoplasmic reticulum, and golgi
apparatus. All their functions take place in the cytoplasm or cytoplasmic
membrane.
 Formed by the words “pro,” which means before, and the Greek word “karyon,”
which means nucleus, nut or kernel.
 Do not have a nucleus or any membrane-bound organelles such as mitochondria,
and their ribosomes (site of protein synthesis) are a smaller size than eukaryotic
ribosomes.
 Their DNA is in a single circular chromosome located in a nucleoid region within the
bacteria cell.
 They have a cell wall made of peptidoglycan that aids bacterial cells in maintaining
their shape and helps in preventing lysis caused by increased osmotic pressure,
Features of the cell wall contribute to the staining properties of bacterial cells.
 The Gram stain is the most widely used stain in microbiology, and the reactions,
gram-positive or gram-negative, correlate to the cell wall structure of bacteria.
 Inside the cell wall is a cell membrane (lipid bilayer that surrounds the cytoplasm),
and many bacteria are enclosed within a polysaccharide or protein capsule, also
called the slime layer.
 An important structure formed by gram-positive bacteria is the spore or endospore.
Bacteria form spores by a process called sporulation when the environment
becomes hostile (e.g., nutrient depletion). Spores are resistant to heat, cold, drying
conditions, and chemicals and therefore are able to survive under extremely
unfavourable conditions.
 Spore-forming bacteria can revert to the vegetative or active state when the
conditions become favorable again. This process is referred to as germination.
 Bacteria have external structures such as fimbriae or pili and flagella. Flagella are
threadlike structures anchored within the cell membrane. The rotational motion
(described as “runs” and “tumbles”) of the flagella enables the bacterial cell
 Pili are hairlike structures on the exterior of bacterial cells that promote adherence
surfaces. For many bacteria, adherence to tissue begins the infection process, and
therefore pili are termed a virulence factor (factor that contributes to the disease
process).
 Eukaryotes
 These are microorganisms that contain a true nucleus (with chromosomes bound by
a nuclear membrane).
 These are cells of higher plants, animals, fungi, protozoa, and other more
morphologically complex and larger organisms than prokaryotes.
 Greek for “true nucleus”
 Are animal, plant, and fungal cells
 They have a membrane bound nucleus, organelles (e.g., mitochondria, lysosomes),
cytoskeleton, cell membrane, and larger ribosomes.

CHARACTERISTICS PROKARYOTES EUKARYOTES

Size of the cell 0.2-2.0 um
Cell wall Usually present
Nucleus Absence of nuclear
membrane or nucleoli
Genome location In the nucleoid or at the
mesosome
Chromosomes Single, singular
chromosomes; without
histones
Membrane-bond organelles Absent
Ribosomes Present; smaller size (70s)
Pili or fimbriae Present
Flagella Simple; consists of two
protein building blocks
Lysosomes and peroxisomes Absent
Sterols Absent (except in
Mycoplasma spp)
Introns in genes Absent
Cytoskeleton and cytoplasmic No cytoskeleton and
streaming cytoplasmic streaming
Gas vesicles Present
Cell division Asexual (binary fission)
10-100
Usually absent except in
fungi (chitin); if present, it
is chemically simple.
True nucleus with nuclear
membrane and nucleoli
In the nucleus
Multiple linear
chromosomes; with
histones
Present
Present; larger size (80s)
Absent
Complex (multiple
microtubules)
Present
Present
Present
With cytoskeleton and
cytoplasmic streaming
Absent
Sexual and asexual

 Archaebacteria
 Archae is from the Greek word “archaics,” which means ancient.
 The cellular structures of archea include the cell wall, plasma membrane
ribosomes, and flagella.
 They do not contain a nucleus and membrane bound organelles.
  The cell walls of archaebacteria never contain peptidoglycan, but they mostly
contain a protein or glycoprotein wall structure known as the “S-layer”
 These organisms are classified as aerobes, facultative anaerobes, or obligate
anaerobes.
 They may be stained either as gram positive or gram negative in various shapes such
as spherical, rod, and spiral (pleomorphic).
 They grow and survive under extreme environmental conditions.
 They reproduce through binary fission, fragmentation, or budding.

 Intramolecular forces
1. Hydrogen bonds
2. Hydrophobic interactions
3. Electrostatic forces
4. van der Waals forces

 Covalent Bond
 A pair of electrons shared between two atoms, ordinarily shown as a straight line
between bonded atoms.
a) Polar covalent bonds
b) Nonpolar covalent bonds
Water and pH
 Water is the predominant chemical component of living organisms.
 The manner in which water interacts with a solvated biomolecules influences the
structure both of the biomolecule and of the water itself.
 pH is the negative log of [H+]. A low pH characterizes an acidic solution, and a high
pH denotes a basic solution.
 Buffers resists a change in pH when protons are produced or consumed.
 Physiologic buffers include bicarbonate, orthophosphate, and proteins.
Water
 Water is the principal component of most cells, comprising about 70% or more of the
weight of most organisms.
 Electronegativity- the tendency of an atom to attract electrons to itself in a chemical
bond.
Water and Polarity
 Electro negativities of Selected Elements

ELEMENTS ELECTRONEGATIVITIES
Oxygen 3.5
Nitrogen 3.0
Sulphur 2.6
Carbon 2.5
Phosphorus 2.2
Hydrogen 2.1
* Electronegativity values are relative, and are chosen to be positive numbers ranging
from less than 1 for some metals to 4 for fluorine.

POLARITY
 When two atoms with the same electronegativity form a bond, the electrons are shared
equally between the two atoms.
 The difference in electronegativity between oxygen and hydrogen give rise to a partial
positive and negative charge.
 Water is a bent molecule with a bond angle 104.3 and the uneven sharing of electrons
in the two bonds is not cancelled out as it is in CO2.
 The result is that the bonding electrons are more likely to be found at the oxygen end of
the molecule than at the hydrogen end. Bonds with positive and negative ends are
called dipoles.
Solvent Properties of Water
 The polar nature of water largely determines its solvent properties.
 The underlying physical principle is electrostatic attraction between unlike charges.
 Ionic and polar substances are referred to as hydrophilic (“water-loving,” from the
Greek) because of this tendency.
 Nonpolar molecules do not dissolve in water and are referred to as hydrophobic
(“water-hating,” from the Greek).
 Hydrocarbons in particular tend to sequester themselves from an aqueous environment.
 Examples of Hydrophilic and Hydrophobic Substance.

HYDROPHILIC HYDROPHOBIC
1. Polar covalent compounds (e.g., 1. Nonpolar covalent compounds (e.g.,
Alcohols such as Ethanol and ketones hydrocarbons such as hexane)
such as Acetone) 2. Fatty acids and Cholesterol
 2. Sugars
3. Ionic compounds
4. Amino acids and phosphate

 Amphipatic- compound that contain regions that are polar (or change) and regions that
are non-polar.
OSMOSIS
 Osmosis is the passage of a solvent through a semipermeable membrane separating a
dilute solution (or pure solvent) from a more concentrated solution.
 A semipermeable membrane is a membrane that allows certain types of molecules to
pass through it but prohibits the passage of other types of molecules.
 Acid- a molecule that acts as a proton (hydrogen ion) donor.
 Base- a molecule that acts as a proton acceptor.
 The degree of dissociation of acids in water, for example, ranges from essentially
complete dissociation for a strong acid to practically no dissociation for a very weak
acid, and any intermediate value is possible.
 Water has a slight propensity to dissociate into hydroxide ions and protons.
 The concentration of protons, or acidity, of aqueous solutions is generally reported
using the logarithmic.

STRUCTURAL ORGANIZATION OF COMPLEX BIOMOLECULES

Inorganic precursors
 THREE-DIMENSIONAL ARCHITECTURE OF BIOMOLECULES
 The structures of any molecule is a unique and specific aspect of its identity
 Weak forces maintain the biological structure and determine biomolecular interactions.

Weak Forces Maintain Biomolecules Structure and Interactions

 Van der Waals Interaction, Hydrogen Bond, Ionic Interaction and Hydrophobic
Interaction.
 These weak forces create interactions that are constantly forming and breaking at
physiological temperature and their collective action stabilize structure and interaction
of biomolecule.

Biomolecular Recognition
 Structural complementarity is the means of recognition in biomolecular interactions.
 The complicated and highly organized patterns of life depend on the ability of
biomolecules to recognize and interact with one another in very specific ways.
 Structural complementarity is the very essence of biomolecular recognition
 E.g., proteins; metabolites; DNA: complementary strand; egg

Weak Chemical Forces Mediate Biomolecular Recognition

 Interactions are sufficiently weak, they are readily reversible
 So that biomolecular interactions that tend to be transient, rigid, static lattices of
biomolecules that might paralyze cellular activities are not formed