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29-Jan-18

Biochemical Engineering
CHE F421
Dr. Amit Jain
BITS Pilani Asst. Prof., Dept. of Chemical Engg.
Pilani Campus
BITS Pilani – Pilani Campus

BITS Pilani
Pilani Campus

Lecture 2 - 4
Basics of Microbiology

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29-Jan-18

Presentation Outline

• Diversity of Microorganisms
• Naming and Taxonomy of Cells
• Procaryotes
• Eucaryotes
• Viruses
• Cell Structure - major classes of compounds
• Culture Media Components

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Microbial Diversity and their


Environment
• Life is very tenacious and can exist in extreme environment.

• Temperature: Some cells can grow at -20oC others at 120oC


• Grows best below 20oC Psychrophiles
• Grows best between 20 and 50oC Mesophiles
• Grows best above 50oC Thermophiles

• pH
• Grows best near neutral pH Neutrophiles or Mesophiles
• Grows well at pH of 1 to 2 Acidophiles
• Grows well at pH as high as 9 Alkaliphile

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Microbial Diversity and their


Environment
• Oxygen Availability:
• Requires oxygen for growth Aerobic
• Requires lack of oxygen for growth Anaerobic
• Aerobic or Anaerobic Facultative

• Nutrient Availability:
• Most cells require Organic and Inorganic nutrients to grow and
survive.
• Cyanobacteria (formerly called blue-green algae) can grow in the
absence of key nutrients
• Can convert CO2 from air into organic cellular molecules.
• Can also convert N2 into NH3 for essential cellular material.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Microbial Diversity and their


Environment
• Organisms from extreme environments (extremophiles)
• Key to maintenance of natural cycles.
• Can be used in recovery of metals from low-grade ores or in the
desulfurization of coke.
• Not only variety of habitats, but also wide range of size
and shapes.
• Spherical or Elliptical Coccus
• Cylindrical Bacillus
• Spiral Spirillum
• Some may change shape in response to their change in
their local environment.
• This great diversity provides immense variety of potential
tools for the engineers. We need to learn to exploit them.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Taxonomy (Naming of Cells)

• Taxonomy is the development of approaches to organize


and summarize our knowledge about the variety of
organisms that exist.
• Necessary for efficient communication.
• Plays a critical role in patent litigation.
• Binary Nomenclature (dual name & are in Latin)
Escherichia coli
species
Genus
(organisms that are
(a group of related species)
substantially alike)
• E. coli B/r A will differ in growth and physiological
properties from E. coli K12.
• Ex. Humans: Homo + Sapiens
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Protist (Unicellular) Kingdom

Protist
Kingdom

Procaryotes Eucaryotes

Blue-green
Bacteria Fungi Algae Protozoa
algae

Molds Yeast

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Primary Subdivision of
Cellular Organisms (Table 2.1)

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Primary Subdivision of
Cellular Organisms (Table 2.2)
Group Cell Properties Constituent groups
Structure
Eucaryotes Eucaryotic Multicellular; extensive Plants (seed plants,
differentiation of cells and ferns, mosses)
tissues Animals (vertebrates,
Unicellular, coenocytic or invertebrates)
mycellial; little or no tissue Protist (algae, fungi,
differentiation protozoa)
Eubacteria Procaryotic Cell chemistry similar to Most bacteria
eucaryotes
Archae- Procaryotic Distinctive cell chemistry Methanogens,
bacteria halophiles, thermo-
acidophiles

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Viruses

Obligate Parasites - not considered life


Structural Components of Viruses
i. Genetic material: DNA (DNA viruses) or RNA (RNA
viruses)
ii. Capsid: a protein coat over the genetic material
iii. Outer envelope: some contain a lipoprotein outer
envelope
Types of Viruses
i. Bacteriophage: virus that infects a bacteria
ii. Plants: tobacco mosaic virus
iii. Humans: polio virus, SARS virus
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Replication of Virulent
Bacteriophage

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Viruses

• A phage attack on an E. coli fermentation causes huge


losses.

• Viruses are used as vectors for the insertion of desired


DNA into a host cell in genetic engineering.

• In some cases a killed virus preparation is used as a


vaccine.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Procaryotes
• Mostly, procaryotes sizes vary from 0.5 to 3 µm.
• Procaryotic cells grows rapidly (t1/2 =~ 30 min to few hrs)
Eubacteria:
• Can be divided into several different groups.
• One distinction is based on gram stain test.
• Other, based on cellular nutrition and energy metabolism.
• Cyanobacteria (blue-green algae) have chlorophyll and fix CO2
into sugars.
• Anoxygenic photosynthetic bacteria (the purple and green
bacteria) have light gathering pigment bacteriochlorophyll.
• Unlike true photosynthesis they do not obtain reducing power from
the splitting of water
• Do not produce oxygen .
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Staining Test

• Developed by Hans Christian Gram.


Procedure:
1. Fix the cells by heating.
2. Add basic dye, crystal violet, all bacteria will stain
purple.
3. Add iodine followed by ethanol. Gram-positive cells will
remain purple, while gram-negative cells becomes
colorless.
4. Counterstaining with safranin (red organic dye) leaves
gram-positive cells purple, while gram-negative cells are
red.
The test reveals the intrinsic structure of the cells.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Gram Staining Test

Gram Positive Bacteria Gram Negative Bacteria

BITS Pilani, Deemed to be University under Section 3 of UGC Act, 1956

Gram Negative Vs Gram


Positive Cells

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Gram Negative Vs Gram


Positive Cells

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Staining Test

Crystal Voilet Dye Peptidoglycane


Tris(4-(dimethylamino)phenyl) by Yikrazuul
-methylium chloride

BITS Pilani, Deemed to be University under Section 3 of UGC Act, 1956

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Gram Staining Test

The four basic steps of the Gram Stain are:


1) Application of the primary stain Crystal Violet (CV) to
a heat-fixed smear of bacterial culture.
• Tris (4-(dimethylamino)phenyl)-methylium chloride
• CV dissociates in aqueous solutions in to CV+ and Cl–
ions.
• These two ions then penetrate through the cell wall
and cell membrane of both Gram-positive and Gram-
negative cells.
• The CV+ ions later interacts with negatively charged
bacterial components and stains the bacterial cells
purple.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Staining Test

2) Addition of Gram’s Iodine.


• Iodine (I– or I3–) acts as a mordant and as a trapping
agent.
• A mordant is a substance that increases the affinity of
the cell wall for a stain by binding to the primary
stain, thus forming an insoluble complex which gets
trapped in the cell wall.
• In the Gram stain reaction, the crystal violet and
iodine form an insoluble complex (CV-I) which serves
to turn the smear a dark purple color.
• At this stage, all cells will turn purple.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Gram Staining Test

3) Decolorization with 95% ethyl alcohol.


• Alcohol or acetone dissolves the lipid outer membrane of Gram
negative bacteria, thus leaving the peptidoglycan layer exposed
and increases the porosity of the cell wall.
• The CV-I complex is then washed away from the thin
peptidoglycan layer, leaving Gram negative bacteria colorless.
• On the other hand, alcohol has a dehydrating effect on the cell
walls of Gram positive bacteria which causes the pores of the
cell wall to shrink.
• The CV-I complex gets tightly bound into the multi-layered,
highly cross-linked Gram positive cell wall thus staining the cells
purple.
• The decolorization step must be performed carefully, otherwise
over-decolorization or under decolorization may occur.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Staining Test

4) Counterstain with Safranin


• The decolorized Gram negative cells can be rendered visible
with a suitable counterstain.
• Usually positively charged safranin is used, which stains Gram
negative cells pink.
• Pink colour which adheres to the Gram positive bacteria is
masked by the purple of the crystal violet

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Gram Negative Bacterium

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Negative Bacterium

A. 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

Pariplasmic space: space between membranes

Flagellum: 10-20 nm thick hair-like structures, provides


mobility
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Gram Negative Bacterium

B. Cytoplasm
Nuclear material: a single chromosome of DNA with no
nuclear membrane.

Ribosomes: sites of protein synthesis. Cells contain


about 10,000 of them. Size is about 10 - 20 nm. 63%
RNA and 37% protein.
Storage granules: storage of key metabolites. 0.5-1 µm
each.

Spores: used by cell to survive harsh conditions of high


heat, dryness, and antibiotic agents. One spore formed
per cell.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Gram Positive Bacterium

• Typical cell, Bacillus subtilis.


• No outer membrane, rather have a thick rigid cell wall
with multiple layers of peptidoglycan.
• Contains teichoic acids covalently bonded to the
peptidoglycan.
• Since they only have cytoplasmic membrane, they are
much better suited to excretion of proteins
(technologically advantageous when protein is a desired
product).

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Primary Eucaryotic Cells

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Eucaryotic Cells

A. 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.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Eucaryotic 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 (ADPATP) occur.
Endoplasmic reticulum: Membrane complex extending from
cell membrane, sites of protein synthesis and
modification.
Lysosomes: Small membrane-bound particles that contain
digestive enzymes.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Eucaryotic Cells

B. Cytoplasm (continued)
Golgi 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: chlorophyll-containing structures that are
responsible for photosynthesis in plants and algae.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Yeast
Fungi
Molds

Yeasts:
• 5-10 µm in size;
• spherical, cylindrical or oval
in shape;
• most common yeast used
in industry is
Saccharomyces cerevisiae,
which is used for:
– Baker’s yeast production
under aerobic conditions, and
– Alcohol production under
anaerobic conditions.

BITS Pilani, Pilani Campus

Fungi

Molds:
• Filamentous fungi with a
mycelial 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.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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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 (chloreila, spirullina) 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.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Protozoa

• Are unicellular, motile,


relatively large (1-50 µm)
eucaryotes that lack a cell wall.
• Usually obtain food by
ingesting other small
organisms.
• They cause a number of
human diseases (malaria,
dysentery – intenstinal infection
causing diarrhoea) but may
have beneficial roles in
removing bacteria from
wastewater.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Thanks for your patience !!

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Cell Construction
 Cells are composed of:
Biopolymers (major structural elements of living cell)
 Proteins - cell wall, cytoplasm as enzyme
 Nucleic acids - cell nucleus as DNA
 Polysaccharides - cell wall
 Lipids - cell wall
 Storage materials - in cytoplasm
(Fats, polyhydroxybutyrate, glycogen)
Inorganic salts or metabolites
NH4+, PO43-, K+, Ca2+, Na+, SO42-
Other intermediates and vitamins
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Cell Composition

Elemental composition of a bacterial cell:


• 50% carbon,
• 20% oxygen,
• 14% nitrogen,
• 8% hydrogen,
• 3% phosphorus,
• 1% sulfur,
• trace: K+ , Na+, Ca2+ , Mg2+ , Cl2- , vitamins.
• Living cell – a complex reactor with approx. 2000 rxns.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Cell Construction

Levels of biological systems analysis for simplified


understanding:
• molecular level (molecular biology, biochemistry);
• cellular level (cell biology, microbiology);
• population level (microbiology, ecology); and
• production level (bioprocess engineering).

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Amino Acids & Proteins


Proteins
 constitute about 40 to 70 % of cell dry weight
 M.W: 6000 to several hundred thousands D (1 Dalton= 1 g/mole.)
 Consists of large amino acid chains (>50)
 Enzymes represents the largest class of proteins.
 2000 different known enzymes.
 Protein conformation:
1. Fibrous proteins
2. Globular protein
 Most enzymes are globular protein.
 Enzymes are highly specific (active site) to substrate,
and have extraordinary catalytic power.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Amino Acids & Proteins

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Amino Acids & Proteins


 Amino acids have
acidic and basic
groups.
 Acidic group:
Neutral at low pH
Negative charged at
high pH
At intermediate pH
amino acid becomes a
dipolar molecule called zwitterion
Zwitterion.
BITS Pilani, Pilani Campus

Common Amino Acids

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Common Amino Acids

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Amino Acids & Protein

Isoelectric point
pH at which amino acids have no net charge
(depends on the R groups)
point, at which amino acid does not migrate under an
electric field
significant for protein purification
 Proteins (c/d conjugated proteins) may consists of
organic and/or inorganic components (c/d prosthetic
groups) other than amino acids.
Ex. Hemoglobin – contains four heme groups (iron
containing organometallic complexes)

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Amino Acids & Protein

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Amino Acids & Proteins

 Amino acids are optically active.


 Isomeric forms:
 L-amino acid (in protein only) and,
 D-amino acid (rare, some MO’s cell wall)

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Concept of Optical Activity

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Amino Acid & Proteins


• Proteins are biopolymers composed of numerous amino
acid units, created through enzyme-mediated condensation
reactions forming a peptide bond.
• (Polypeptides: <50 amino acids)

Peptide Bond
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Proteins: Diverse Biological


Functions
1. Structural proteins: glycoproteins, collagen,
keratin
2. Catalytic proteins: enzymes
3. Transport proteins: hemoglobin, serum
albumin
4. Regulatory proteins: hormones (insulin, growth
hormone)
5. Protective proteins: antibodies, thrombin

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Hierarchy of protein structure

• Primary structure
• Sequence of amino acids
• Secondary structure
• These are formed by hydrogen bonding between amino
acid side chains and formation of α-helix or β-sheet
• Tertiary structure
• 3-dimensional structure of the protein, including an
active site (in case of enzyme), disulfide bonds.
• Quaternary structure
• if the protein contains more than one polypeptide chain
(or subunit) the collective structure is the quaternary
structure.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Protein Structure

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Amino Acids & Proteins


Antibodies or Immunoglobulins
 Are proteins that bind to foreign
macromolecules (antigens) with
high specificity (immune response).
Industrial Applications
• diagnostic kits
• protein separation
• drug delivery
Research Areas
 How cells develop and produce
antibodies.
 How to impart catalytic activity to
antibodies (such AB’s are c/d abzymes)
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Carbohydrates, Lipids, Fats


and Steroids
• Synthesized by photosynthesis. Energy source for many,
but not all organisms.
• Classification of carbohydrates [(CH2O)n, where n>=3]:
• Monosaccharides contain 3-9 carbons
• Disaccharides (condensation of two mono s.)
• Polysaccharides (condensation of many mono s.)
• Oligosaccharides (releases mono s. on complete hydrolysis)
• Lipids are hydrophobic biological compounds:
• Water insoluble
• Soluble in non polar solvents (benzene, chloroform, ether)
• Fats are esters of fatty acids with glycerol.
• Steroids are hormones and can also be classified as lipids.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

• Nucleic Acids are the polymers of Nucleotides.


• There are two types of Nucleic Acids: DNA and
RNA.
DNA= deoxyribose nucleic acid
RNA= ribonucleic acid
• DNA encodes hereditary information.
• DNA also encodes information for maintenance
of cell functions.
• RNA is an intermediate used to synthesise
proteins.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA

• Composed of monomers - nucleotides

nucleotide

*Ribose in RNA
Deoxyribose in DNA

•Ribose + Nitrogen base = Nucleoside


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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

Ribose

Deoxyribose
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA

NITROGEN BASES

* Thymine in DNA
**Uracil in RNA

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA


NITROGEN BASES

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA:


Example of a Nucleoside

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA:


Example of a Nucleoside
Nucleosides in DNA

Base Sugar Nucleoside


Adenine (A) Deoxyribose Adenosine
Thymine (T) Deoxyribose Thymidine
Guanine (G) Deoxyribose Guanosine
Cytosine (C) Deoxyribose Cytidine

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA:


Example of a Nucleoside
Nucleosides in RNA

Base Sugar Nucleoside


Adenine (A) Ribose Adenosine
Uracil (U) Ribose Uridine
Guanine (G) Ribose Guanosine
Cytosine (C) Ribose Cytidine

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

Structure of DNA & RNA


Chains.

Phosphodiester bonds are


formed between 3’ and
5’ carbon atoms.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA

SECTION OF RNA

Backbone of
RNA consists of pentoses
and phosphate groups.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

Features of Double Helix of DNA


• DNA contains two strands of
nucleotides.
• H bonds hold the two strands in a
double-helix structure.
• A helix structure is like a spiral
stair case.
• Bases are always paired as A–T
and G-C.
• Thus the bases along one strand
complement the bases along the
other.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA


• The phosphate and deoxyribose units are on the outer
surface, but the bases point toward the chain center.
• The planes of the bases in the chain are perpendicular
to the helix axis.
• The diameter of the helix is 2 nm.
• The helical structure repeats after ten residues on each
chain, at an interval of 3.4 nm.
• The two chains are held together by hydrogen bonding
between pairs of bases.(A-T: two H bonds, G-C: three H
bonds).
• This feature is essential to the genetic role of DNA.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

DNA Replication
• DNA in the chromosomes replicates itself every
cell division
• Maintains correct genetic information
• Two strands of DNA unwind
• Each strand acts like a template
• New bases pair with their complementary base
• Two double helixes form that are copies of
original DNA

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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DNA Replication

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

Roles of RNA Species


• Messenger, m-RNA: Synthesized on the
chromosome and carries genetic information for
protein synthesis.
• Transfer, t-RNA: Carries specific amino acid
from cytoplasm to the site of protein synthesis
on ribosomes.
• Ribosomal, r-RNA: Part of machinery of protein
synthesis, constituets about 65% of total
ribosomes.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Nucleic Acids, RNA, & DNA

RNA Structure
• Most RNA molecules have secondary structure,
consisting of stem & loop domains.
• Double helical stem domains arise from base
pairing between complementary stretches of
bases within the same strand.
• Loop domains occur due to lack of
complementarity or the presence of modified
bases prevents base pairing.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Nucleic Acids, RNA, & DNA

“Cloverleaf” model of tRNA.

Identity elements: acceptor stem


& anticodon loop.

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Cell Nutrients to be taken up


in Next Class

// Thanks //

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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Cell Nutrients

carbon source 50%


nitrogen source 14%
oxygen source 20%
Macronutrients hydrogen 8%
phosphorus 3%
sulfur 1%
potassium, magnesium

Micronutrients Fe, Zn, Mn, Cu, Co, Mo, Ca, Na, Cl, Ni,
Se, and others
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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Growth Media

• Defined
• are very specific recipes in which certain ingredients must be
present in specific amounts.
• Complex
• Complex media are composed of partially digested yeast, beef,
soy and additional proteins, in which the exact concentration and
composition is unknown.
• Selective
• Selective media contain ingredients that inhibit the growth of
certain types of bacteria and/or encourage the growth of others
• Differential
• Differential culture media are formulated to display a color
change when the bacteria growing metabolize a certain
ingredient.
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Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

Story of Penicillin

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History of Penicillin

 Typical example for implementation of biotechnology


 Inhibiting the formation of peptidoglycan cross-links
in the bacterial cell wall : Inhibition of D,D-transpeptidase

Penicillin G (Benzyl penicillin)


R = benzyl group

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Discovery and bioprocess development


 Alexander Fleming : tried to isolate the bacterium, Staphylococcus
aureus, by growing it on the surface of nutrient at St. Mary’s
Hospital in 1928
 Breakthrough in the antibiotic history

• He noticed that no bacteria grew near the invading substance in


the contaminated plate : The cell killing must be due to an
antibacterial agent
- Not a failed experiment, but a meaningful finding

• Identification of foreign particles as common mold of the


Penicillium genus (later identified as Penicillium notatum)

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 Recovery and test of a tiny quantity of secreted material using the


crude extraction methods : powerful antimicrobial activity and
named “penicillin”
- The discovery laid essentially dormant for over a decade

 World War II resurrected the discovery : desperate demand for an


antibiotic with minimal side effects and broad applicability
• Howard Florey and Ernst Chain of Oxford : rebuilt on Fleming’s
observation

• They produced enough penicillin to treat some laboratory animals :


Treat of a London policemen for a blood infection
 Great efficacy against infection

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 The supply of penicillin was exhausted


- Need a process to make large amounts of penicillin
- Process development required engineers, microbiologists,
and life scientists
- Approached pharmaceutical companies in the USA like
Merck, Pfizer, Squibb, and to develop the capacity to
produce penicillin at large amount

• First attempt : chemical synthesis of penicillin because of a


great deal of success with other drugs
- Chemical synthesis : proved to be extremely difficult
- Fermentation process : an unproved approach

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 The War Production Board appointed A.L. Elder to coordinate the


activities of penicillin producers to greatly increase the supply of
penicillin in 1943
 Commercial production of penicillin by a fermentation process

 Problems : very low concentration (titer) of penicillin


- In 1939, the final concentration of penicillin in broth : ~0.001 g/L

-Low rate of production per unit volume: Low productivity


 very large and inefficient fermentors

- Difficult with product recovery and purification


- Fragile and unstable penicillin  constraints on
recovery and purification methods
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 Major contribution to the penicillin program by NRRL


• Development of a corn steep liquor-lactose based medium 
ten-fold increased productivity

• Isolation of a new strain (> few hundreds) :


Penicillium chrysogenum

• Other hurdles : Manufacturing process


- Growth of the mold on the surface of moist bran
- Growth of the mold on top of a liquid medium ;
requires many milk bottles  Bottle plant  long
growing cycle and labor intensive

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 Submerged fermentation process : Challenges


- Mold physiology : productivity vs conditions
- Reactor design : reactor size and configuration,
oxygen supply (low solubility of oxygen, viscosity,
mixing, mass transfer ), heat removal, agitator design,
mechanical sealing, decontamination,

 Product recovery/purification : pH shift and liquid-liquid extraction

 First plant for commercial production by Pfizer


 100,000 gal scale in 1945

 Nobel prize in 1945 for three scientists


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Reactors for submerged culture

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 Accomplishment required a high level of multidisciplinary work


Ex) Merck assigned a engineer and microbiologist together to each
aspect of the problem

 Continued progress with penicillin fermentation through


physiology, metabolic pathway engineering, mold genetics,
process control, reactor design:
- Increase from 0.001 to ~ 100 g/L

 Production of penicillin derivatives with greater potency:


Antibiotic resistance
- Semi-synthetic antibiotics
- Protein engineering to design relevant enzymes:
More economically feasible process

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Biosynthesis of Penicillin G in Fungus

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Penicillin F

Penicillin G
Enzymatic process

Protein Engineering

Penicillin nucleus
(6-APA)

Derivatives (rational design)


Animal test
Clinical trials (Phase I, II, III)

New antibiotics with greater potency


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Derivatives of β-lactam antibiotics

Amoxicillin
Ampicillin Flucloxacillin

Dicloxacillin
Methicillin Carbenicillin

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29-Jan-18

Lessons from the penicillin story

• Analysis of the failed experimental results in a critical way:


Curiosity leads to a creative and original idea

• Demand for economic feasibility leads to the development of


more efficient bioprocess

• The development of biological process requires a high level of


inter-disciplinary work

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Thanks for your patience !!

92
Dr Amit Jain, Asst. Prof., Dept. of Chemical Engg., BITS Pilani

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