Chapter 2: An Overview of Biological Basics

Prof. Zakaria Al-Qodah

Department of Chemical Engineering

Faculty of Engineering Technology

Summer Semester (2019-2020)

Presentation Outline: Lectures 2 and 3
Diversity of Microorganisms

Naming and Taxonomy of Cells

Prokaryotes
Eukaryotes
Viruses
Cell Structure- major classes of compounds
Culture Media Components
 Diversity of Microorganism:
Environmental Conditions
Temperature
I.Grows best below 20˚C Phychrophiles
II.Grows best between 20 and 50˚C Mesophiles
III.Grows best above 50˚C Thermophiles
IV Grows best above 70˚C Extreme thermophiles

pH
I.Grows best near neutral pH
II.Grows well at pH of 1 to 2 Acidophiles
III.Grows well at pH as high as 9
 Diversity of Microorganism:
Environmental Conditions
Moisture
i. Most cells require a minimum moisture content
ii. Some cells grow in the near absence of moisture

Salinity
i. Most cells require a moderate level of salinity
ii. Some cells can exist in very high salt concentrations
 Diversity of Microorganism:
Environmental Conditions
Oxygen Availability
Require oxygen for growth Aerobic
Require lack of oxygen for growth Anaerobic
Switch from aerobic or anaerobic Facultative

Nutrient Availability
Most microorganisms require organic and inorganic nutrients to
grow and survive
Cyanobacteria (blue-green algae) grow in the absence of key
nutrients: e.g. can convert CO2 from air into organic cellular
molecules (Photosynthetic).
The can convert N2 and NH3 to essential building blocks
 Diversity of Microorganism:
Cell Morphology

Size and Shape

Spherical or Elliptical coccus cocci

Cylindrical bacillus Bacilli

Spiral spirillum spirilla

.
 Benefits of Microorganism Diversity

Microorganisms that able to survive in extreme

conditions are called Extremophiles

Important tools to produce chemicals and medicinals

They are key to the maintenance of natural cycles

Can be used for the recovery of metals,

desulphurization of coal or oil
Treatment of highly toxic materials

.
 Naming of Cells (Nomenclature)
Taxonomy: Concerned with approaches for
classification
Nomenclature: The actual naming of microorganisms

Cell Names are in Latin or latinized

A genus is a group of related species

Genus Name: Escherichia

Species Name: coli
Full name Escherichia coli
Abbreviated name: E. coli
Exact name: E. coli K12 is different from E. coli B/r A
 Taxonomy of Cells
Table 2.1 .
 Taxonomy of Cells
Table 2.2

.
 Procaryotic cells: Procaryotes

Size from 0.5-3 μm equivalent radius

Different species and shapes

Spherical or coccus Staphylococci
Cylindrical or bacillus E. coli
Spiral or spirillum Rhodospirillum

Use different nutrients including carbon sources such

as carbohydrates, protein, hydrocarbon and CO2

.
 Procaryotic cells
I.Eubacteria

Gram –ve
Gram +ve

II. Archaebacteria live in extreme environments and

process unusual metabolism such as:
Methanogens
Thermoacidophiles
 Gram Stain, Hans Christian Gram
The procedure

Fixing by heat

Staining with crystal Violet

Add Iodine
All cells become purple

Add ethanol
Gram +ve cells remain purple
Gram –ve become colorless
Counterstaining with safranin
Gram +ve remains purple
Gram –ve become red
 Gram Stain, continued

Gram -ve cells have outer cell membranes

This membrane prevents the crystal violet from entering the
cell
Ethanol washing removes the stain
Safranin find place to attach
Gram +ve cells do not have outer cell membranes
crystal violet enters the cell and reacts with its biomolecules
Ethanol washing can not remove the stain
Safranin does not find place to attach
 Gram –ve bacteria

Gram -ve cells have outer cell membranes

This membrane prevents the crystal violet from entering the
cell
Ethanol washing removes the stain
Safranin find place to attach
Gram +ve cells don not have outer cell membranes
crystal violet enters the cell and reacts with its biomolecules
Ethanol washing can not remove the stain
Safranin does not find place to attach
Gram +ve vs Gram -ve
 Eucaroyates: Eucarutic cells
A.Cell Envelope - provides rigidity
Cell wall: animal cells have no cell wall (fragile).
Plant cells have a wall containing peptidoglycan, Cellulose and
polysaccharides
Plasma membrane: phospholipid bilayer structure with imbedded
proteins similar to Procaryotes. Major difference is the presence of
sterols, which impart rigidity.
 Eucaroyates: Eucarutic cells

B. Cytoplasm
Nucleus: chromosomes surrounded by a membrane.

Mitochondria: 1-3 μm cylindrical bodies. The powerhouses of

the cell where respiration and oxidative phosphorylation
occur.

Endoplasmic reticulum: Membrane complex extending from

cell membrane, sites of protein synthesis and modification.

Lysosomes: Small membrane-bound particles that contain

digestive enzymes.
 Eucaroyates: Eucarutic cells

B. Cytoplasm (continued)

Glogi bodies: small particles composed of membrane
aggregates responsible for excretion of proteins and other
products.

Vacuoles: membrane bound organelles of plant cells

responsible for nutrient digestion, osmotic regulation, and
waste storage.

Chloroplasts: chlorophyl-containing structures that are

responsible for photosynthesis in plants and algae.
 Fungi
Yeasts
5-10 μm in size;
Spherical, cylindrical or oval in shape.
Most common yeast is Saccharomyces cerevisiae, which is used for
baker’s yeast production under aerobic conditions and for alcohol
production under anaerobic conditions.
 Fungi
Molds
Filamentous fungi with a mycellial structure.
Mycelium is a highly branched system of tubes that contain
mobile cytoplasm with many nuclei.
Molds are used for production of citric acid and many
antibiotics.
 Algae
Single or multi-celled organisms that contain chloroplasts and perform
photosynthesis.
Size is 10 - 30 μm. Diatoms contain silica in their cell walls and are used
as filter aids in industry.
Some algae are used in the wastewater treatment industry with
simultaneous production of single-cell protein.
Certain gelling agents such as agar and alginic acid are obtained from
marine algae and seaweed.
 Protozoa
Are unicellular, motile, relatively large (1-50 μm)
Eucaryotes that lack a cell wall.
They cause a number of human diseases (malaria, dysentery) but may
have beneficial roles in removing bacteria from wastewater.
.
 Viruses
Obligate Parasites - not considered life

Structural Components of Viruses

Genetic material: DNA (DNA viruses) or RNA (RNA viruses)
Capsid: a protein coat over the genetic material
Outer envelope: some contain a lipoprotein outer envelope

Types of Viruses
Bacteriophage: virus that infects a bacteria
Plants: tobacco mosaic virus
Humans: polio virus, SARS virus
Presentation Outline: Lectures 3 and 4

Amino Acids and Proteins

Carbohydrates
Lipids, Fats and Steroids
Nucleic Acids (DNA and RNA
Plasmids
Cell Composition
Cell Culture Macronutrient Elements
Cell Culture Defined medium
Cell Culture Complex Medium
 Cell Construction
A- Amino Acids and proteins

 Amino acids are the building blocks (monomers) of proteins and enzymes.

 Amino acids have acidic (-COOH) and basic (-NH2) groups.

 Only L-amino acids are manufactured in cells and incorporated into
proteins. Some D-amino acids are found in the cell walls of bacteria,
but not in bacterial proteins.
zwitterion

Both groups can exchange protons (H+) and alter the

charge as a function of pH.

This pH - charge behavior allows for their separation

using a column apparatus.
There are 21 Amino Acids:
 Amino Acids: Peptide Linkage
Proteins are biopolymers composed of numerous amino acid units,
created through enzyme-mediated condensation reactions forming
a peptide bond or linkage
 Proteins: Prosthetic Groups

In addition to amino acids:

 proteins can also contain organic or inorganic
components termed prosthetic groups. For example,
 hemoglobin contains four heme groups (iron-containing
organometallic complex).
 Prosthetic groups can impart catalytic activity to proteins.
 Proteins containing prosthetic groups are termed
conjugated proteins.
 Primary Structure of proteins

Linear sequence, type of amino acids and number

Secondary Structure of proteins
Hydrogen bonds between far groups
 Tertiary Structure of proteins
3-dimensional form of the protein. Interactions of R groups far apart
on the chain (hydrogen, covalent, ionic and disulfide bonding).
 Quaternary Structure of proteins
It refers to how these protein subunits interact with each other and arrange
themselves to form a larger aggregate protein complex.
Protein primary, secondary, tertiary and
quaternary structure
 Proteins (Continued)
 The mass of proteins is often given in terms of Daltons
 A protein having a molecular mass of 150 kilo Daltons has a Mo.
M. of (150,000)(1.00797)=151,195.5 grams / mole of protein.

Protein Function
 Structural proteins (collagen, keratin, glycoproteins)
 Catalytic proteins (enzymes)
 Transport proteins (hemoglobin, serum albumin)
 Regulatory proteins hormones (insulin, growth hormone)
 Protective proteins (antibodies, thrombin)
 B- Carbohydrates
 Carbohydrates are compounds containing carbon, oxygen,
and hydrogen.
 They are created by photosynthesis primarily from plants by
fixation of CO2 using energy from sunlight.
 Their general formula is (CH2O)n where n = 3.
Monosaccharaides

Tow main categories:

 Aldoses and Ketoses

Two Main Isomers

D (Dextro)
L (Levo)
 Monosaccharaides
 Two main structures: Open and Closed Chain
 Two Closed structures α (36%) and β (64%)
 Disaccharides
 Disaccharides are formed by condensation reactions
between two monosaccharaides
Polysaccharides: starch
Structure of cellulose and starch
 Polysaccharides
 Polysaccharides are formed by condensation reactions between two
or more mono-saccharides linked by glycosidic bonds.
 C- Lipids, Fats and Steroids
Lipids are different heterogeneous biomolecule that is soluble in
nonpolar solvents
Fatty Acids
Saturated and unsaturated fatty acids
 Formation of Fats and Oils
By the reaction of three fatty acid units with glycerol, a trihydroxy
alcohol Triglyceradehide is formed
steroids structures
 D- Nucleic Acids (DNA and RNA)
Nucleotides are the building blocks of DNA and RNA. They are
composed of a sugar (ribose or deoxyribose), phosphate, and a N base
Primary Structure of DNA
DNA Duplication
Cell Composition
Cell Culture Macronutrient Elements
Cell Culture Media