CH-412

Bio Chemical
Engineering

Dr. Faizan Raza

Assistant Professor
Department of Chemical Engineering
NED University of Engineering & Technology

March 7th, 2019

CLO’s & PLO’s

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 Course Syllabus
➢ Basic of Microbiology
➢ Enzyme Classification
➢ Enzyme reaction kinetics (Single substrate Reactions) and
energy patterns in biological system
➢ Enzyme Inhibition
➢ Nonideal Enzyme Kinetics, Isolation of enzymes and
immobilized enzyme technology
➢ Applications of Enzyme Catalysis (Biocatalysis)
➢ Transport phenomenon in microbial system
➢ Design and analysis of biochemical reactors (fermentators)
➢ Anaerobic and aerobic metabolism photosynthesis and bio
synthesis
➢ Biochemical and microbiological application to commercial
and engineering. 3/21
 Books
1. Biochemical Engineering Fundamentals by J. E. Bailey
& D. F. Ollis, McGraw Hill Book Company, 1986.

2. Biochemical Engineering by H. W. Blanch & D. S. Clark,

Marcel Dekker, Inc., 1997.

3. Bioprocess Engineering (Basic Concepts) by M. L.

Shuler & F. Kargi, Prentice Hall of India, 2003.

4. Biochemical Engineering and Biotechnology by Ghasem

D. Najafpour, Elsevier, 2007

5. Organic Chemistry 7th edition, 2007 by John McMurry

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Google Classroom

www.classroom.google.com

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 Chapter 1.
Industrial Microbiology

Book:
Biochemical Engineering and Biotechnology by
Ghasem D. Najafpour, Elsevier, 2007

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Microorganisms

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Microorganisms
▪ Microorganisms have been identified and exploited for
more than a century.

▪ There is a great history beyond fermentation processes,

which explains the applications of microbial processes
that resulted in the production of food and beverages.

▪ In the mid-nineteenth century, Louis Pasteur understood

the role of microorganisms in fermented food, wine,
alcohols, beverages, cheese, milk, yoghurt and other
dairy products, fuels, and fine chemical industries.

▪ He discovered the first principal role of fermentation,

which was “that microbes required substrate to produce
primary and secondary metabolites, and end products”.
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 Process Fermentation
➢ The term ‘fermentation’ was obtained from the Latin verb ‘fervere’,
which describes the action of yeast or malt on sugar or fruit
extracts and grain.
➢ The ‘boiling’ is due to the production of carbon dioxide bubbles
from the aqueous phase under the anaerobic catabolism of
carbohydrates in the fermentation media.
➢ Fermentation is known as a process with the existence of strictly
anaerobic life: that is, life in the absence of oxygen.
The process is summarised in the following steps:
❖ Action of yeast on extracts of fruit juice or, malted grain. The
biochemical reactions are related to generation of energy by
catabolism of organic compounds.
❖ Biomass or mass of living matter, living cells in a liquid solution
with essential nutrients at suitable temperature and pH leads to cell
growth. As a result, the content of biomass increases with time.
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Process Fermentation

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Application of Fermentation Processes

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Application of Fermentation Processes

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Application of Fermentation Processes

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Chapter 26.
Amino Acids, Peptides
& Proteins.

Book:
Organic Chemistry 7th edition, 2007 by John McMurry

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Introduction: Amino Acids, Peptides & Proteins

Proteins:
• They occur in every living organism.
• They are of many different types.
• They have many different biological functions.
✓ Keratin of skin and fingernails: key structural material.
✓ Fibroin of silk and spider webs
✓ Estimated 50,000 to 70,000 enzymes that catalyze the biological
functions of the human body
→ They are all proteins.

• Regardless of their functions, all proteins are made up of many amino

acids linked together in a long chain.

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Amino Acids, Peptides & Proteins
◆ Amino acids are difunctional as their name implies.
→ Contain both a basic amino group and an acidic carboxyl group.

→ We can join together into long chains by forming amide bonds between
the –NH2 of one amino acid and the –CO2H of another.
• Peptides are chains with fewer than 50 amino acids.
• Proteins are large chains of amino acids, more than 200 amino acids.

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1.1 Structures of Amino Acids
◆ A carboxyl group is deprotonated and exists as the carboxylate anion at a
pH of 7.3 (the physiological pH), while an amino group is protonated and
exists as the ammonium cation.
→ Amino acids exist in aqueous solution primarily in the form of a dipolar
ion, or
zwitterion.
Zwitterion:
• German zwitter, meaning “hybrid”.
• A neutral dipolar molecule with both the positive and negative charges at
different locations within that molecule.

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Structures of Amino Acids
◆ Amino acid zwitterions are internal salts and therefore have many of the
physical properties associated with salts.
→ Have large dipole moments.
→ Are soluble in water but are insoluble in hydrocarbons.
→ Are crystalline substances with relatively high melting points.

◆ Amino acids are amphiprotic:

→ They can react as acids or as bases, depending on the circumstances.

→ In aqueous acid solution, an amino acid zwitterion is a base that accepts
a proton (Fig.1)
→ In aqueous basic solution, an amino acid zwitterion is a acid that loses a
proton (Fig.2).
Fig.1 Fig.2

Basic site
Acidic site
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Structures of Amino Acids
◆ The structures, abbreviations and pKa values of the 20 amino acids
commonly found in proteins are shown in the table below.

Three-letter One-letter

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Structures of Amino Acids

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Structures of Amino Acids

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Structures of Amino Acids

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Structures of Amino Acids
◆ All 20 amino acids found in proteins are -amino acids.
→ The amino group in each is a substituent on the  carbon atom – the one
next to the carbonyl group.
→ 19 of the amino acids are primary amines, RNH2.
✓ Differ only in the side chain, the substituent attached to the  carbon.
✓ Proline, a secondary amine, is the only amino acid whose nitrogen and 
carbon atoms are part of the ring.

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 Structures of Amino Acids
◆ In addition to the twenty amino acids commonly found in proteins, two
others – selenocysteine and pyrrolysine – are found in some organism,
and more than 700 non-protein amino acids are also found in nature.

✓ Non-protein amino acids:

→ −Aminobutyric acid (GABA) is found
in the brain and acts as a
neurotransmitter.
→ Homocysteine is found in the blood
and is linked to coronary heart
disease.
.
→ Thyroxine is found in the thyroid gland
and acts as a hormone
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Structures of Amino Acids
◆  Carbons of amino acids are chirality centers, except for glycine, H2NCH2CO2H.
→ Two enantiomers of each are therefore possible.
→ Nature uses only one enantiomer to build proteins: often referred to as L-
amino acids.
→ The non-naturally occurring enantiomers are called the D-amino acids.

Tetrahedral
carbon

a) ✓ The molecules (a, b) are identical to their

mirror images.
→ you can superimpose one on the other.
b) ✓ However, the molecule (c) is not identical to
its mirror image.
→ you can’t superimpose one on its mirror
c) image.
→ this is kind of stereoisomer called
Mirror images enantiomer.

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 Structures of Amino Acids
◆ Look at the three remaining substituents in figure below. The numbers indicates the
order of priorities → 4 is the group of lowest priority.
• R configuration
→ If a curved arrow drawn (1 → 2 → 3) through substituents is clockwise, after
the group of lowest priority points directly back (Newman projection).
• S configuration
→ If a curved arrow drawn (1 → 2 → 3) through substituents is counterclockwise.

◆ Sequence rule for specifying configuration:

• Rule 1:
→The atom with the highest atomic number is
ranked first; the atom with the lowest atomic
number (usually hydrogen) is ranked fourth.
• Rule 2:
→ If a decision cannot be reached by ranking the
first atoms in the substituents, look at the
second, third, or fourth atoms outward until a
difference is found.
ex) (-OH) > (-CO2H) > (-CH3)
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Structures of Amino Acids
Ex) Newman projection

→ The modern nomenclature usually employs the prefixes R and S.

→ The old-fashioned nomenclature still uses “D” and “L”.
→ “R = D” clockwise, “S = L” counterclockwise.
→ In proteins, a L-form of amino acids are used.

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Structures of Amino Acids
◆ The 20 common amino acids can be further classified as acidic, basic, or

neutral, depending on their side chains.

→ two (aspartic acid and glutamic acid) of the 20 have an extra carboxylic acid
function in their side chains: they are so acidic that they can be deprotonated at
physiological pH (7.3).
→ Three (lysine, arginine, and histidine) have basic amino groups in their side
chains: they are so basic that they can be protonated at pH 7.3.
→ Fifteen have neutral side chains.
→ Cysteine with a thiol, and tyrosine with a phenol, have weakly acidic side
chains that can be deprotonated in a sufficiently basic solution.
→ However, histidine with a heterocyclic imidazole ring is not quite basic enough to
be protonated at pH7.3.

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Structures of Amino Acids
• Each carbon of pyrrole contributes one  electron and the sp2-hybridized nitrogen contributes two from its
lone pair.
→ Less available for binding
.

• The five carbon atoms and the sp2-hybridized nitrogen atom of pyridine contribute one 
electron to the aromatic sextet.

<

More basic

✓ Only the pyridine-like nitrogen is basic, the pyrrole-like nitrogen is non-

basic because its lone pair of electrons is part of the 6 electron aromatic
imidazole ring.
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