CHAPTER 1 BASIC BIOLOGY FOR ENGINEER

Microbial diversity
Taxonomy
Cell naming
Gram Stain

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 Schematic Overview of A Biotechnological Processes

Organism
selection

Applied Genetics: mutation,

recombination, gene, gene manipulation

Air Energy

Raw Materials:
Bioreactor: microbial, animal or Downstream processing:
selection, pretreatment
plant cells, or enzymes product separation & purification
& Preparation

heat Product
isolated
Sterilization Process Control

Formulation
processing
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 Microbial Diversity
1. Temperature
v Psychrophiles (grow best < 20oC)
v Mesophiles (grow best at 20 - 50oC)
v Thermophiles (grow best at >50oC)

2. Oxygen
v Aerobic- require O2 for growth
v Anaerobic – growth inhibited by O2, best to grow without O2
v Facultative – organism that can switch the metabolic pathways to allow
them to grow under either circumstance.
v Anoxic: condition with very low free O2

3. Extreme environment
v Cyanobacteria (blue green algae) – can grow with no obvious source of
nutrient, photosynthetic that can convert CO2 from atmosphere into
organic compounds, can convert N2 into NH3.
v Extremophiles – organism grow in extreme environment

4. Size and Shape

v Coccus – spherical or elliptical shape
v Bacillus – cylindrical or rod shape
v Spirillium- spiral shape
Some cells may change shape in response to changes in their
environment.
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 Naming Cells
Cell name in latin
— A genus: a group of related species
— A species: includes organisms that are substantially
alike.
e.g. Escherichia coli; Bacillus subtilis; Sacchromyces
cerevisiae; Penicillium chrysogenum. (in italic type)

Various strain and substrains are designated by the addition of letters and
numbers. e.g. E. coliK12
Microorganisms Taxonomy
— Bacteria
— Fungi (yeast, mold)
— Algae
— Protozoa
— Viruses
— Animal

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Microorganisms Taxonomy
— Bacteria

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 Gram Staining
— In 1884, Hans Christian Gram, a Danish doctor working in
Berlin, accidentally stumbled on a method which still forms
the basis for the identification of bacteria.
— While examining lung tissue from patients who had died of
pneumonia, he discovered that certain stains were
referentially taken up and retained by bacterial cells.
— Over the course of the next few years, Gram developed a
staining procedure which divided almost all bacteria into
two large groups – the Gram stain.
 Gram Staining
— Gram staining (or Gram's method) is a method of differentiating
bacterial species into two large groups (Gram-positive and Gram
negative).
— It is based on the chemical and physical properties of their cell walls.
— It detects peptidoglycan, which is present in a thick layer in Gram
positive bacteria.
— A Gram positive results in a purple/blue color while a Gram negative
results in a pink/red color
— The outer membrane can be then permeabilized by acetone
treatment, and the pink safranin counterstain is trapped by the
peptidoglycan layer.
 Gram positive bacteria
• Simple cell wall
— Gram positive bacteria – stained with colors due to cell wall
structure
— Surrounded by cytoplasmic membrane covered by a
structural murein network composed of polysaccharides and
amino acids
— Cytoplasmic membrane - phospholipids double layer
(deformable)
— Murein layer is quite rigid and maintain characteristic shape
of bacterium
— murein layer is much thicker than gram (-)
— gram (+) is more difficult to disrupt mechanically
— particularly susceptible to lysis by the antibacterial enzyme
lysozyme
— Eg: Lactobacillus and Staphylococcus

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 Gram negative bacteria
— Complex cell wall – multi layered envelops
— Murein layer (peptidoglycan) of cells wall is thinner and
surrounded by outer membrane
— Eg Escherichia coli and Pseudomonas
— Outer membrane
— Peptidoglycan
— Lipopolysaccharides + proteins
— Periplasm
— Liquid filled gap
— Important in bioprocessing
– recombinant proteins are secreted into it
– use osmotic shock to recover

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 E.Coli, P.aeruginosa
gram negative (pink red)
Gram Positive – Gram Negative

Murein layer (10-80 nm)

Cytoplasmic membrane (8 nm)

Periplasmic space

Outer membrane (8 nm)

Murein layer

Cytoplasmic membrane (8 nm)

Periplasmic space

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Gram negative Gram positive
CELLULAR ORGANISM

Prokaryotes & Eukaryotes

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Cellular Organism
Cells — 2 Types: Prokaryotic and Eukaryotic
— Prokaryotic = no membrane-enclosed nucleus
— bacteria
— gram positive- stain with crystal violet
— gram negative – weak stain with crystal violet

— Eukaryotic = has nuclei and internal organelles

— yeast,
— animal
— plant
— fungi (mold)

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 Prokaryotic Cells

Eukaryotic and Prokaryotic Cells

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Classification of Cells: Cell Wall

— Cell without cell wall

— animal
— Cells with cell wall
— bacteria
— fungi (mold)
— yeast
— plant

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 Procaryote
— Procaryotes have no membrane around the cell genetic
information and no membrane-bound organelles
— Contain single chromosomes; contain no organelles like
mitochondria, endoplasmic, recticulum
q Bacteria: e.g. E. Coli, Rhodospirillum sp.
q Size: 0.5 to 3 μm, can be >600μm

— Grow rapidly: e.g. one cell can replicate into over a

million cells in just 12 hours. In contrast, a human cell
takes 24 hours to split.
— Utilize carbon sources: carbohydrates, hydrocarbon,
protein and CO2.
Prokaryotes: Bacteria

— Gram negative: outer cell wall covered by peptidogylcan, eg:

E.coli,
— Gram positive: have cell wall
— Cytoplasm: 50% protein, 30% lipid and 20% carbohydrate
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 Procaryote - Gram Negative Cells
Cell Envelope
— Outer membrane: 10 – 20 nm thick, a protein-polysaccharide lipid complex
— Inner membrane: 5-10 nm thick, 50% protein - 30% lipid – 20%carbohydrate
— Periplasmic space: space between membranes
— Flagellum: 10-20 nm thick hair-like structures, provides mobility
Cell wall
— Eubacteria cell walls contain lipids & peptidoglycan which is a complex polysaccharide with
amino acids and forms a structure somewhat like chainlink fence.
— Archaebacteria cell walls do not have peptidoglycan.
Pilus (Pili, pl.)
— A pilus is a hairlike structure on the surface of a cell.
— Pili enable the transfer of plasmids between the bacteria.
— An exchanged plasmid can add new functions to a bacterium, e.g., an antibiotic
resistance.
Cytoplasm
— The cytoplasm is surrounded by a membrane called cytoplasmic membrane.
— The cytoplasmic membrane contains 50% protein, 30% lipids and 20% carbohydrates.

Gram negative microorganism = Escherichia coli, Salmonella, Shigella, Pseudomonas, Moraxella,

Helicobacter, Bdellovibrio, acetic acid bacteria, Legionella and Wolbachia.
 Procaryote - Gram Positive Cells
— Examples: Bacillus,Listeria,Staphylococcus,
Streptococcus, Enterococcus, and Clostridium.
— No outer membrane
— Has very thick, rigid cell wall with multiple layer
of peptidoglycan
— Contain teichoic acids covalently bond to
peptidoglycan
— Have only cytoplasmic membrane - suitable for
excretion of proteins
Prokaryotes
2 types:
1) Eubacteria-various industrially important
organisms, and mycoplasma, which are currently an
enemy for mammalian cell culture enthusiasts)
2) Archeabacteria:
— Methanogens
— Thermoacidophiles
— halobacteria

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 Eukaryotic Cells
— Yeast (unicellular), mold cells (multicellular,
filamentous)
— Thick cell walls (highly crosslinked structure)- Mainly
composed of polysaccharides (glucans, mannans and
chitins)
— Plasma membranes – composed of phospholipids and
lipoproteins
— Mammalian (Animal) cells
Eukaryotic = — Animal cells do not have cell walls
has nuclei — Animal cells are very fragile
and internal
— Cultured animal cells are several microns in size
organelles
— Spherical or ellipsoid
•yeast
•fungi (mold) — Plant cells
•animal — Very thick cell wall (cellulose and other polysaccharides)
•plant

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 Eukaryotic Cells
— Plant cells
— can be bigger
— Cell Wall - thick and robust
— composed of cellulose and other polysaccharides
— difficult to disrupt
— Cultured plant cells are less robust than real plant
cells

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 Eucaryotes
— Eucaryotes complex than prokaryotic since has
organelles in cytoplasm
— Eucaryotes include fungi (yeast and molds), algae,
protozoa, and animal and plant cells.
— Eucaryotic cells are bigger than procaryotic cells in
diameter.
— Yeast is about 5 -10 μm, animal 10 μm and plant 20
μm.
 Eucaryotes
— Cell Envelope - provides rigidity
— Cell wall: animal cells have no cell wall (fragile).
— Plant cells have a wall containing peptidoglycan,
polysaccharides and cellulose.
— Plasma membrane: phospholipid bilayer structure with
imbedded proteins similar to procaryotes.
— Major difference is the presence of sterols, which impart
rigidity.
— Eucaryotes contain sterol which strengthen the wall
structure and make the membrane less flexible.
— The cell wall of eucaryotes shows variations. e.g.
q Fungi contain chitin ,
q Plant cells contain cellulose
q Animal cells do not have cell wall (only cytoplasmic membrane) so
that they are shear sensitive and fragile.
Eucaryotes
 Eucaryotes
Cytoplasm
— Nucleus: chromosomes surrounded by a membrane.
— Mitochondria: 1-3 μm cylindrical bodies. The power houses 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.
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.
Characteristics of eucaryotes: organelles

— nucleus (with nuclear membrane); contain

chromosomes and histones
— mitochondria (powerhouse of eucaryotes):
responsible for respiration, oxidative phosphorylation
— endoplasmic reticulum (convoluted membranes lead
from cell membrane into cell):
— rough (contain ribosomes, responsible for protein
production)
— smooth (site of lipid synthesis)
— lysosomes (membrane-bound small organelles:
release digestive enzymes
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Yeasts
—Saccharomyces cerevisiae are commonly known as
brewers or bakers yeast
—brewers yeast: ethanol production from sugars under
anaerobic conditions (production of wine, beer and
whiskey (distilled after fermentation)
— bakers yeast: production of CO2 under aerobic
conditions.

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MOLDS
— grow on surfaces
— can also grow in submerged culture
— classified by method of reproduction
— produce citric acid, penicillin and other antibiotics

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Components of cells
— important to know for culture media development
— bacterial cell (approximate, average values): 50%
carbon, 20% oxygen, 14% nitrogen, 8% hydrogen,

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Summary
— Introduction to Biochemical Engineering
— Issues and role as Biochemical engineers
— History and regulations
— Chapter 1 Basic Biology:
— microbial diversity, taxonomy, cell naming, gram stain
— cellular organism - prokaryotes, eukaryotes

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 System Biology
— Simultaneous examined complex interaction
between components, phenomena in
cell/organism.
1. Genes
2. Proteins
3. Metabolites
4. Cell cycle
5. Signaling

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 Metabolic pathways
Series of consecutive enzymatic reactions that
produce specific products.
—Metabolites - reactants, intermediates, products
—Anabolism – biosynthesis
Few metabolites (pyruvate, acetyl-CoA, citric acid
cycle intermediates) serve as starting materials
—Catabolism – degradation
Diverse substances converted to common
intermediates, which lead to acetyl-CoA

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 Characteristics of metabolic
pathways:
1. Almost all metabolic reactions are reversible.
2. Metabolic pathways however, are irreversible.
3. Metabolic pathways have irreversible steps.
4. All metabolic pathways are regulated.
5. Metabolic pathways in eukaryotic cells occur in
specific cellular locations.

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THANK YOU

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