Biochemical Engineering PDF

15/09/2018
Biochemical
Engineering
Engr. Peter Fowler
Biochemical Engineering
• Introduction
• Biomolecules
• Cells and Microorganisms
• Enzymes and Enzyme Kinetics
• Bioreactor Design
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Introduction
Introduction
• Biochemical engineering, or bioprocess
engineering, makes use of living cells and their
components, such as enzymes, to manufacture new
products and destroy harmful wastes.
• The use of microorganisms to transform biological
materials or production of fermented foods has been
around since antiquity.
• Our ability to harness the capabilities of cells and
enzymes is closely related to advances in
biochemistry, microbiology, immunology, and cell
physiology.
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Introduction
Introduction
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Introduction
Introduction
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Introduction
Introduction
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Introduction
• The interdisciplinary nature of bioprocess
engineering becomes obvious when we look at the
stages of development of a complete industrial
bioprocess.
• The first stages may involve genetic engineering of
microbes to produce wanted products.
• The next stage may involve microbiological techniques to
optimize growth conditions for the microbes.
• Then, bench-top bioreactors are used to scale-up the
process.
• The system is scaled-up again to pilot-scale bioreactors to
examine scale-up effects of performance.
• Finally, design of the industrial-scale operation ensues.
Introduction
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Biomolecules
Nucleotides and Nucleic Acids

• Nucleotides are the monomers of nucleic acids.
• There are eight common varieties, each composed of a
nitrogenous base linked to a sugar with at least one
phosphate group attached.
• The bases are planar, aromatic, and heterocyclic:
either purine or pyrimidine.
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• The most common purines are:
• adenine (A)
• guanine (G)
• The most common pyrimidines are:
• cytosine (C)
• uracil (U)
• thymine (T)
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• In ribonucleotides (for RNA), the
sugar is a pentose known as ribose.
• In deoxyribonucleotides (for
DNA), the sugar is also a pentose
known as deoxyribose.

• The best-known nucleotide is adenosine
triphosphate, ATP.
• a nucleotide containing adenine, the sugar ribose, and a
triphosphate group
• formed from adenosine diphosphate, ADP
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• When the phosphate group is absent, the
compounds are known as nucleosides.
• Ribonucleotides are components of ribonucleic
acid, RNA.
• Deoxyribonucleotides are components of
deoxyribonucleic acid, DNA.

• The phosphates of the polynucleotides RNA and
DNA are acidic, so at physiological pH, nucleic acids
are polyanions.
• The linkages between individual nucleotides are
known as phosphodiester bonds.
• The phosphate is esterified to two ribose units.
• The 5’ end corresponds to the nucleotide whose C5’ is
not linked to another nucleotide.
• The 3’ end refers to the nucleotide whose C3’ is not
linked to another nucleotide.
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• DNA forms a double helix, as
determined by James Watson and
Francis Crick in 1953 using an X-
ray diffraction photograph taken
by Rosalind Franklin.
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• RNA is single-stranded, and usually forms compact
structures. Intramolecular base-pairing gives rise to
stem-loop structures.
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Amino Acids and Proteins

• Amino acids are monomers of proteins.
• There are 20 “standard” amino acids.
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• Amino acids are linked to each other via
condensation reactions, forming peptide bonds.
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• Peptides may be dipeptides, tripeptides,
oligopeptides, or polypeptides.
• Polypeptides are linear polymers, not branched.
• The residue with the free amino group is called the
amino terminus or N-terminus.
• The residue with the free carboxylate group is called the
carboxyl terminus or C-terminus.
• PROTEINS are molecules that contain one or more
polypeptide chains.
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Carbohydrates
• Carbohydrates or saccharides are the most
abundant biological molecules.
• They are chemically simpler than nucleotides and amino
acids, containing only C, H, and O.
• These elements are combined according to the formula
(CH2O)n, where n > 3.
• The basic carbohydrate units are monosaccharides.
• These can be strung together to form disaccharides,
oligosaccharides, or polysaccharides.
Carbohydrates
• Monosaccharides are aldehyde or ketone
derivatives of straight-chain polyhydroxy alcohols
containing at least three carbons.
• If the carbonyl group is an aldehyde, the sugar is an
aldose.
• If the carbonyl group is a ketone, the sugar is a ketose.
• The smallest monosaccharides, with three carbons,
are trioses. Those with four, five, six, seven, etc. are
called tetroses, pentoses, hexoses, heptoses, etc.
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Carbohydrates
• The stereochemistry of carbohydrates is assigned by
D or L.
• D sugars have the same absolute configuration at the
asymmetric center farthest from their carbonyl group as
does D-glyceraldehyde.
• L sugars are biologically much less abundant than D
sugars.
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Carbohydrates
• The hydroxyl and either the aldehyde or the ketone
functional groups of monosaccharides can react
intramolecularly to form cyclic structures.
• A sugar with a six-membered ring is called as a pyranose.
• A sugar with a five-membered ring is called as a furanose.
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Carbohydrates
• Disaccharides are the simplest polysaccharides,
consisting of two monosaccharide units.
• Monosaccharides are joined to other monosaccharides
via glycosidic bonds.
• Lactose is a disaccharide of glucose and galactose. It is
found naturally occurring in milk. It is also a reducing
sugar.
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Carbohydrates
• Disaccharides are the simplest polysaccharides,
consisting of two monosaccharide units.
• Sucrose is a disaccharide of glucose and fructose. It is
commonly known as table sugar. It is non-reducing.
Carbohydrates
• Cellulose, the primary structural component of
plant cell walls, is a linear polymer of up to 15,000
D-glucose residues.
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Carbohydrates
• Chitin, the principal structural component of
invertebrate exoskeletons, is a polymer of N-acetyl-
D-glucosamine residues.
Carbohydrates
• Carbohydrates are used as substrates for
fermentation, producing ethanol.
• Prior to fermentation, the monosaccharide, C6,
passes through the glycolytic pathway which splits
it into two C3 molecules.
• These molecules are then directed into the anaerobic
fermentation pathway, yielding two C2 molecules
(ethanol) and two C molecules (carbon dioxide).
C6H12O6 ⟶ 2CH3CH2OH + 2CO2
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Lipids
• Lipids are substances of biological origin that are
soluble in organic solvents such as chloroform and
methanol.
• fats, oils, certain vitamins and hormones, most
nonprotein membrane components
• In general, they perform three biological functions:
• as essential components of biological membranes
• as energy stores
• as participants in cell signaling events
Lipids
Fatty Acids
• carboxylic acids with long-chain hydrocarbon side groups
• Saturated fatty acids are highly flexible molecules.

• The melting points of saturated fatty acids increase with
molecular mass.
• Unsaturated fatty acids almost always have cis
double bond configurations.
• This results to less efficient packing and therefore lower
melting points.
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Lipids
Triglycerides (triacylglycerols)
• fatty acid triesters of glycerol
• Most triglycerides contain two or three different

types of fatty acid residues.
• Fats and oils are complex mixtures of triglycerides
whose fatty acid compositions vary with the
organism that produced them.
• Plant oils are usually richer in unsaturated fatty acids
than animal fats.
Lipids
Steroids
• derivatives of cyclopentanoperhydrophenanthrene
• cholesterol – the most abundant steroid in animals;
classified as a sterol because of its C3-OH group
• major component of animal plasma membranes
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Lipids
Steroids
• derivatives of cyclopentanoperhydrophenanthrene
• steroid hormones – substances that control a great
variety of physiological functions
• glucocorticoids – affect carbohydrate, protein, and lipid
metabolism, as well as influence other vital functions
such as inflammation and coping with stress (e.g.
cortisol)
• mineralocorticoids – regulate the excretion of salt and
water by the kidneys (e.g. aldosterone)
• androgens and estrogens – affect sexual development
and function (e.g. testosterone, estradiol)
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Lipids
Isoprenoids
• derived from five-carbon units with the same carbon
skeleton as isoprene
• Over 50,000 isoprenoids (also known as
terpenoids), which are mostly of plant, fungal, and
bacterial origin, have been characterized.
• vitamin A – retinol
• vitamin K – pylloquinone or menaquinone
• vitamin E – α-tocopherol
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Lipids
Eicosanoids
• C20 compounds including prostaglandin,
thromboxanes, leukotrienes, and lipoxins
• act at very low concentrations and are involved in the
production of pain and fever, and in the regulation of
blood pressure, blood coagulation, and reproduction
• In humans, the most important eicosanoid
precursor is arachidonic acid.
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Review Questions and Problems

#1
These are the most abundant organic molecules in
living cells.
(a) proteins
(b) carbohydrates
(c) lipids
(d) fats

#1
These are the most abundant organic molecules in
living cells.
(a) proteins
(b) carbohydrates
(c) lipids
(d) fats
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#3
Which of the following is not a steroid?
(a) sex hormones
(b) cholesterol
(c) adrenocortical hormones
(d) prostaglandin

#3
Which of the following is not a steroid?
(a) sex hormones
(b) cholesterol
(c) adrenocortical hormones
(d) prostaglandin
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#15
Genetic information is stored in the structure of the
DNA molecule. Which of the following obtains the
code for protein synthesis from DNA and serves as the
template for peptide formation?
(a) transfer RNA
(b) messenger RNA
(c) ribosomal RNA
(d) codon

#15
Genetic information is stored in the structure of the
DNA molecule. Which of the following obtains the
code for protein synthesis from DNA and serves as the
template for peptide formation?
(a) transfer RNA
(b) messenger RNA
(c) ribosomal RNA
(d) codon
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#22
Which of the following amino acids is basic?
(a) alanine
(b) lysine
(c) serine
(d) cysteine

#22
Which of the following amino acids is basic?
(a) alanine
(b) lysine
(c) serine
(d) cysteine
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#24
An aqueous solution of molasses contains 15%
sucrose (C12H22O11). The CO2 formed in the reaction
can be considered as having a negligible solubility in
the solution. Determine % ethanol in solution after
95% of the sucrose has been converted to ethyl
alcohol by fermentation.
(a) 2.07%
(b) 4.14%
(c) 7.67%
(d) 8.28%

#24
An aqueous solution of molasses contains 15%
sucrose (C12H22O11). The CO2 formed in the reaction
can be considered as having a negligible solubility in
the solution. Determine % ethanol in solution after
95% of the sucrose has been converted to ethyl
alcohol by fermentation.
(a) 2.07%
(b) 4.14%
(c) 7.67%
(d) 8.28%
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#25
Albizzia falcataria, a specie of plywood, after an initial
thermochemical hydrolysis yielded 25% maltose, 3% sucrose,
12% cellobiose, 43% oligosaccharides, and 17% non-
carbohydrate residues. The resulting hydrolysate is passed
through a column of immobilized enzyme systems so that all
types of disaccharides are converted further to hexose units. In
alcohol fermentation, the rule of thumb is 10% of the substrate
is converted to biomass and 90% to alcohol. What mass of
ethanol is expected to be produced per six-day week if one
metric ton of pulpwood is processed daily?
(a) 1162 kg
(b) 1223 kg
(c) 1885 kg
(d) 2526 kg

#25
Albizzia falcataria, a specie of plywood, after an initial
thermochemical hydrolysis yielded 25% maltose, 3% sucrose,
12% cellobiose, 43% oligosaccharides, and 17% non-
carbohydrate residues. The resulting hydrolysate is passed
through a column of immobilized enzyme systems so that all
types of disaccharides are converted further to hexose units. In
alcohol fermentation, the rule of thumb is 10% of the substrate
is converted to biomass and 90% to alcohol. What mass of
ethanol is expected to be produced per six-day week if one
metric ton of pulpwood is processed daily?
(a) 1162 kg
(b) 1223 kg
(c) 1885 kg
(d) 2526 kg
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#29
One metric ton of wild potatoes were hydrolyzed
enzymatically and the hydrolysate contained the
following: xylose, 2%; pentose, 3%; glucose, 16%;
maltose, 20%; oligosaccharides, 36%; others, 23%. It was
observed that of the hydrolysate, only maltose and glucose
were fermentable by alcohol yeast. Calculate the mass of
alcohol that can theoretically be produced from the
hydrolysate.
(a) 95 kg
(b) 189 kg
(c) 338 kg
(d) 371 kg

#29
One metric ton of wild potatoes were hydrolyzed
enzymatically and the hydrolysate contained the
following: xylose, 2%; pentose, 3%; glucose, 16%;
maltose, 20%; oligosaccharides, 36%; others, 23%. It was
observed that of the hydrolysate, only maltose and glucose
were fermentable by alcohol yeast. Calculate the mass of
alcohol that can theoretically be produced from the
hydrolysate.
(a) 95 kg
(b) 189 kg
(c) 338 kg
(d) 371 kg
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#30
Hydrolysis of one mole of sucrose gives
(a) 1 mole of glucose and 1 mole of galactose
(b) 1 mole of glucose and 1 mole of fructose
(c) 2 moles of glucose
(d) 1 mole of mannose and 1 mole of glucose

#30
Hydrolysis of one mole of sucrose gives
(a) 1 mole of glucose and 1 mole of galactose
(b) 1 mole of glucose and 1 mole of fructose
(c) 2 moles of glucose
(d) 1 mole of mannose and 1 mole of glucose
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#31
The isoelectric point of isoleucine (2.36, 9.68) is:
(a) 6.02
(b) 6.06
(c) 5.98
(d) 5.97

#31
The isoelectric point of isoleucine (2.36, 9.68) is:
(a) 6.02
(b) 6.06
(c) 5.98
(d) 5.97
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#35
The color of fruits like papaya is attributed to a
pigment which is a precursor of Vitamin A. This
substance is:
(a) lecithin
(b) carotene
(c) lipoprotein
(d) riboflavin

#35
The color of fruits like papaya is attributed to a
pigment which is a precursor of Vitamin A. This
substance is:
(a) lecithin
(b) carotene
(c) lipoprotein
(d) riboflavin
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#36
A hormone secreted by the pancreas that regulates
glucose metabolism is called:
(a) bile
(b) insulin
(c) alanine
(d) cortisol

#36
A hormone secreted by the pancreas that regulates
glucose metabolism is called:
(a) bile
(b) insulin
(c) alanine
(d) cortisol
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#37
The disaccharide formed by a β-glycosidic bond is:
(a) sucrose
(b) lactose
(c) maltose
(d) glucose

#37
The disaccharide formed by a β-glycosidic bond is:
(a) sucrose
(b) lactose
(c) maltose
(d) glucose
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#40
This is the only natural source of vitamin D.
(a) sunlight
(b) meat
(c) fish oil
(d) orange

#40
This is the only natural source of vitamin D.
(a) sunlight
(b) meat
(c) fish oil
(d) orange
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#41
Calculate the isoelectric point of lysine.
pKa1 = 2.18, pKa2 = 8.95, pKa3 = 10.53
(a) 9.74
(b) 7.22
(c) 6.36
(d) 5.57

#41
Calculate the isoelectric point of lysine.
pKa1 = 2.18, pKa2 = 8.95, pKa3 = 10.53
(a) 9.74
(b) 7.22
(c) 6.36
(d) 5.57
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#42
Which of the following vitamins is water-soluble?
(a) Vitamin C
(b) Vitamin A
(c) Vitamin D
(d) Vitamin E

#42
Which of the following vitamins is water-soluble?
(a) Vitamin C
(b) Vitamin A
(c) Vitamin D
(d) Vitamin E
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#45
The fundamental cause of sickle-cell disease is a
change in the structure of:
(a) red blood cells
(b) hemoglobin
(c) capillaries
(d) blood

#45
The fundamental cause of sickle-cell disease is a
change in the structure of:
(a) red blood cells
(b) hemoglobin
(c) capillaries
(d) blood
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#46
It is the major form of stored carbohydrate in animals.
(a) glycogen
(b) starch
(c) amylose
(d) amylopectin

#46
It is the major form of stored carbohydrate in animals.
(a) glycogen
(b) starch
(c) amylose
(d) amylopectin
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#47
Which of the following is a saturated fatty acid?
(a) oleic acid
(b) linoleic acid
(c) arachidonic acid
(d) palmitic acid

#47
Which of the following is a saturated fatty acid?
(a) oleic acid
(b) linoleic acid
(c) arachidonic acid
(d) palmitic acid
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#48
This is a measure of the degree of unsaturation of a
fatty acid.
(a) acid number
(b) iodine number
(c) saponification number
(d) Deborah number

#48
This is a measure of the degree of unsaturation of a
fatty acid.
(a) acid number
(b) iodine number
(c) saponification number
(d) Deborah number
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Cells and
Microorganisms
Microbial Cell Structure

• All cells have a permeability barrier called the
cytoplasmic membrane that separates the inside
of the cell, the cytoplasm, from the outside.
• The cell wall lends structural strength to a cell; it is
relatively permeable and a much stronger layer than
the membrane itself.
• Plant cells and most microorganisms have cell walls,
whereas animal cells do not.
• prokaryotes – Bacteria and Archaea; DNA is
“naked”
• eukaryotes – algae, protozoa, protists, fungi; DNA is
contained in an organelle (nucleus)
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Microbial Cell Structure

• nucleus – contains the DNA of eukaryotic cells
• mitochondria – site for cellular respiration;
“powerhouse” of eukaryotic cells
• chloroplasts – chlorophyll-containing organelles of
eukaryotic cells
• endoplasmic reticulum – network of membranes
involved in lipid and glycoprotein syntheses
• Golgi complex – chemical modification and sorting
of products from the endoplasmic reticulum
• lysosomes – compartments of digestive enzymes
that hydrolyze proteins, fats, and sugars
Energy Classes of Microorganisms

• chemotrophs – organisms that conserve energy
from chemicals
• chemoorganotrophs – use organic chemicals
• chemolithotrophs – use inorganic chemicals
• phototrophs – organisms that convert light energy
into chemical energy
• photoorganotrophs – use light for energy, organic
chemicals for carbon
• photolithotrophs – use light for energy, inorganic
chemicals (CO2) for carbon
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Energy Classes of Microorganisms

• aerobes – obtain energy from an organic compound
only in the presence of oxygen
• anaerobes – obtain energy only in the absence of
oxygen
• facultative aerobes – obtain energy in either the
presence or absence of oxygen
Cell Growth Kinetics

• The rate of cell growth varies depending on the
growth phase.
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• lag phase
• occurs immediately after inoculation of the culture; rate
of growth essentially zero
• adaptation to the new environment
• acceleration phase
• transition into the growth phase
• growth phase
• growth achieves its maximum rate

• decline phase
• slowing down of growth due to depletion of nutrients in
culture or accumulation of inhibitory products
• stationary phase
• growth ceases; no further growth occurs
• death phase
• (for some cultures); cells lose viability or are destroyed
by lysis
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• During the growth and decline phases (phases
where there is growth), the rate of cell growth is
described by the equation:
𝒓𝒙 = 𝝁𝒙
where rx is a volumetric rate of biomass production,
x is the viable cell concentration, and
μ is the specific growth rate
• In a closed system,
𝒅𝒙
= 𝒓𝒙
𝒅𝒕
EXPONENTIAL GROWTH

• The specific growth rate depends on the
concentration of nutrients in the medium.
• Often, a single substrate exerts a dominant influence on
the rate of growth: the growth-limiting substrate.
This relationship between growth rate and

concentration of nutrients is given by the
MONOD EQUATION:
𝝁𝒎𝒂𝒙𝒔
𝝁=
𝑲𝒔 + 𝒔
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usual conditions:
KS << s
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#2
These are bacteria considered to be ancient
organisms, such as methanogens, halobacteria, and
thermoacidophiles.
(a) archaebacteria
(b) eubacteria
(c) bacteriophage
(d) virus

#2
These are bacteria considered to be ancient
organisms, such as methanogens, halobacteria, and
thermoacidophiles.
(a) archaebacteria
(b) eubacteria
(c) bacteriophage
(d) virus
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#5
Bacteria which convert alcoholic solutions to vinegar
are:
(a) coli
(b) acetobacters
(c) bacilli
(d) proteins

#5
Bacteria which convert alcoholic solutions to vinegar
are:
(a) coli
(b) acetobacters
(c) bacilli
(d) proteins
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#6
The biological decomposition of organic matter
accompanied by the production of foul-smelling
products in an anaerobic condition is:
(a) pollution
(b) putrefaction
(c) dissolution
(d) stabilization

#6
The biological decomposition of organic matter
accompanied by the production of foul-smelling
products in an anaerobic condition is:
(a) pollution
(b) putrefaction
(c) dissolution
(d) stabilization
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#7
A waste treatment process by which biologically
active growth is continuously circulated with
incoming biodegradable waste in the presence of
oxygen:
(a) activated sludge process
(b) stabilization process
(c) agitation process
(d) trickling filter process

#7
A waste treatment process by which biologically
active growth is continuously circulated with
incoming biodegradable waste in the presence of
oxygen:
(a) activated sludge process
(b) stabilization process
(c) agitation process
(d) trickling filter process
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#8
The temperature at which a microorganism is killed
within a period of 10 minutes is called:
(a) SCP
(b) TDP
(c) TDT
(d) ATP

#8
The temperature at which a microorganism is killed
within a period of 10 minutes is called:
(a) SCP
(b) TDP (thermal death point)
(c) TDT
(d) ATP
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#10
A visible concentrated growth of algae or other
aquatic life/plants is called:
(a) phytoplankton
(b) amoeba
(c) bloom
(d) zooplankton

#10
A visible concentrated growth of algae or other
aquatic life/plants is called:
(a) phytoplankton
(b) amoeba
(c) bloom
(d) zooplankton
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#11
Materials in which microorganisms are grown in a
laboratory are:
(a) nutrients
(b) substrates
(c) enzymes
(d) culture media

#11
Materials in which microorganisms are grown in a
laboratory are:
(a) nutrients
(b) substrates
(c) enzymes
(d) culture media
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#14
This is the early period of growth where the organism
adjusts to its new environment.
(a) stationary phase
(b) logarithmic phase
(c) lag phase
(d) decline phase

#14
This is the early period of growth where the organism
adjusts to its new environment.
(a) stationary phase
(b) logarithmic phase
(c) lag phase
(d) decline phase
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#18
For a given species of microorganism that doubles
every 3 h, what is the mass of biomass that may be
expected from 100 liters of seed if each liter contains
8 grams biomass and the fermentation culture was
maintained for 24 h?
(a) 102 kg
(b) 204 kg
(c) 306 kg
(d) 408 kg

#18
For a given species of microorganism that doubles
every 3 h, what is the mass of biomass that may be
expected from 100 liters of seed if each liter contains
8 grams biomass and the fermentation culture was
maintained for 24 h?
(a) 102 kg
(b) 204 kg
(c) 306 kg
(d) 408 kg
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#20
The organism that reproduces by sporulation is:
(a) bacteria
(b) molds
(c) protozoa
(d) yeast

#20
The organism that reproduces by sporulation is:
(a) bacteria
(b) molds
(c) protozoa
(d) yeast
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#21
An organism that grows or uses CO2 as its principal
carbon source:
(a) autotroph
(b) aerobe
(c) mesophile
(d) heterotroph

#21
An organism that grows or uses CO2 as its principal
carbon source:
(a) autotroph
(b) aerobe
(c) mesophile
(d) heterotroph
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#23
The time to kill all bacteria in a particular culture at a
specified temperature:
(a) SCP
(b) TDP
(c) TDT
(d) ATP

#23
The time to kill all bacteria in a particular culture at a
specified temperature:
(a) SCP
(b) TDP
(c) TDT (thermal death time)
(d) ATP
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#26
Bacteria which grow over the temperature range of
30oC to 40oC are called:
(a) psychrophiles
(b) hydrophiles
(c) mesophiles
(d) thermophiles

#26
Bacteria which grow over the temperature range of
30oC to 40oC are called:
(a) psychrophiles
(b) hydrophiles
(c) mesophiles
(d) thermophiles
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#27
This is a group of microorganisms that grow in the
presence of low oxygen concentrations.
(a) pathogens
(b) bacteria
(c) fungi
(d) microaerophiles

#27
This is a group of microorganisms that grow in the
presence of low oxygen concentrations.
(a) pathogens
(b) bacteria
(c) fungi
(d) microaerophiles
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#28
These are very small bound particles that release
digestive enzymes and contribute to the digestion of
nutrients in a cell.
(a) endoplasmic reticulum
(b) Golgi bodies
(c) lysosomes
(d) mitochondria

#28
These are very small bound particles that release
digestive enzymes and contribute to the digestion of
nutrients in a cell.
(a) endoplasmic reticulum
(b) Golgi bodies
(c) lysosomes
(d) mitochondria
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#32
This is the method used to free milk from disease or
germs.
(a) lyophilization
(b) pasteurization
(c) fermentation
(d) putrefaction

#32
This is the method used to free milk from disease or
germs.
(a) lyophilization
(b) pasteurization
(c) fermentation
(d) putrefaction
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#33
The powerhouse of the cell is called the:
(a) nucleus
(b) mitochondrion
(c) lysosome
(d) cytoplasm

#33
The powerhouse of the cell is called the:
(a) nucleus
(b) mitochondrion
(c) lysosome
(d) cytoplasm
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#34
The microorganism utilized in the production of
pickles is:
(a) acetobacter
(b) lactic acid bacteria
(c) Streptomyces griseus
(d) Aspergillus sojae

#34
The microorganism utilized in the production of
pickles is:
(a) acetobacter
(b) lactic acid bacteria
(c) Streptomyces griseus
(d) Aspergillus sojae
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#38
In phototrophic cells, this is the organelle serving as
the major cell powerhouse.
(a) mitochondria
(b) chloroplast
(c) lysosomes
(d) Golgi bodies

#38
In phototrophic cells, this is the organelle serving as
the major cell powerhouse.
(a) mitochondria
(b) chloroplast
(c) lysosomes
(d) Golgi bodies
73
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#44
Plants that are devoid of chlorophyll and are therefore
unable to synthesize their own food are called:
(a) fungi
(b) bacteria
(c) viruses
(d) none of these

#44
Plants that are devoid of chlorophyll and are therefore
unable to synthesize their own food are called:
(a) fungi
(b) bacteria
(c) viruses
(d) none of these
74
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#49
These are DNA or RNA-coated proteins that may or
may not be considered as living things.
(a) protozoa
(b) bacteria
(c) algae
(d) viruses

#49
These are DNA or RNA-coated proteins that may or
may not be considered as living things.
(a) protozoa
(b) bacteria
(c) algae
(d) viruses
75
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#50
These are non-photosynthetic, highly-organized
eukaryotes with soil as their major habitat.
(a) fungi
(b) viruses
(c) protozoa
(d) bacteria

#50
These are non-photosynthetic, highly-organized
eukaryotes with soil as their major habitat.
(a) fungi
(b) viruses
(c) protozoa
(d) bacteria
76
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Enzymes and
Enzyme Kinetics
Properties of Enzymes
• Enzymes are nature’s catalysts.
• specific proteins that enhance biochemical reactions
• Enzymes differ from ordinary chemical catalysts in
several important aspects:
• higher reaction rates
• milder reaction conditions
• greater reaction specificity
• capacity for regulation
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• Enzymes are commonly named by appending the
suffix –ase:
• to the name of the enzyme’s substrate, or
• to a phrase describing the enzyme’s catalytic action
• Enzymes are classified and name according to the
nature of the chemical reactions they catalyze.
• oxidoreductases
• transferases
• hydrolases
• lyases
• isomerases
• ligases
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Enzyme Kinetics
• The kinetics of most enzyme reactions are
reasonably well represented by the model:
𝑘 𝑘1 𝑘𝑐𝑎𝑡
−1
𝐸+𝑆 𝐸∙𝑆 𝐸+𝑃
from which is derived the
MICHAELIS-MENTEN EQUATION
𝒗𝒎𝒂𝒙𝒔
𝒗=
𝑲𝒎 + 𝒔
where v is the volumetric rate of reaction,
s is the substrate concentration,
vmax is the maximum rate of reaction,
and Km is the Michaelis constant.
Enzyme Kinetics
• The Michaelis constant Km is equal to the
concentration at which:
𝒗𝒎𝒂𝒙
𝒗=
𝟐
• Analysis of the reaction sequence also yields the
relationship:
𝒗𝒎𝒂𝒙 = 𝒌𝒄𝒂𝒕 𝑬 𝟎
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Enzyme Kinetics
• first order region:
𝒗𝒎𝒂𝒙
𝒗≈ 𝒔
𝑲𝒎
• zero-order region:
𝒗 ≈ 𝒗𝒎𝒂𝒙
Enzyme Kinetics
• The rate of enzyme reactions depends on the
amount of enzyme present.
• However, enzymes are not always available in pure form
so that [E]0 is unknown.
• In this case, the amount of enzyme can be expressed as
units of activity.
• international unit of enzyme activity (IU) – the
amount of enzyme needed to convert 1 μmole of
substrate into products per minute under standard
conditions
• katal (kat) – SI unit; amount of enzyme required to
convert 1 mole of substrate per second
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Enzyme Kinetics
• For an enzyme with a
single rate-controlling
step, the effect of
temperature can be
described by the
Arrhenius expression:
𝐸𝑎
−
𝑣𝑚𝑎𝑥 = 𝐴𝑒 𝑅𝑇
Arrhenius plot for inversion of sucrose

by yeast invertase
Enzyme Kinetics
• The temperature change over which the
Arrhenius equation is applicable is quite limited.
• Many proteins start to denature at 45 to 50oC.
• If the temperature is raised higher, thermal
deactivation occurs and the reaction velocity drops
quickly.
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Enzyme Kinetics
Enzyme Kinetics
• pH also has a
pronounced effect
on enzyme
kinetics.
• Typically, the
reaction rate is
maximum at some
optimal pH and
declines sharply if
the pH is shifted
to either side of
the optimum
value.
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Enzyme Kinetics
• To specify fully the kinetics of Michaelis-Menten
reactions, both vmax and Km must be known.
• The first step in the kinetic analyses of enzyme
reactions is to obtain data for the rate of reaction v
as a function of substrate concentration data.
• Typically, only initial rate data are used.
• Experimental conditions, such as the enzyme and
substrate concentrations, are known most accurately at
the beginning of reactions.
• Data are then estimated from a direct Michaelis-
Menten plot or several forms of linear plots.
Enzyme Kinetics
Michaelis-Menten Plot
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Enzyme Kinetics
• Lineweaver-Burk Plot
𝟏 𝑲𝒎 𝟏 𝟏
= +
𝒗 𝒗𝒎𝒂𝒙 𝒔 𝒗𝒎𝒂𝒙
• Eadie-Hofstee Plot
𝒗 𝒗𝒎𝒂𝒙 𝒗
= −
𝒔 𝑲𝒎 𝑲𝒎
• Langmuir (Hanes-Woolf) Plot
𝒔 𝑲𝒎 𝒔
= +
𝒗 𝒗𝒎𝒂𝒙 𝒗𝒎𝒂𝒙
Enzyme Kinetics
• Eisenthal-Cornish-Bowden Plot
• v vs s on the negative horizontal axis
84
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#4
In an experiment conducted to evaluate the Michaelis-Menten
constant, it was found that 1 g of bacteria could decompose the
waste at a maximum rate of 35 g/day when the waste
concentration was high. It was also found that the same
quantity of bacteria would decompose waste at a rate of 18
g/day when the waste concentration was 20 mg/L. Calculate
the rate of waste decomposition by 2 g of bacteria if the waste
concentration were maintained at 8 mg/L.
(a) 10.4 g/day
(b) 15.6 g/day
(c) 20.8 g/day
(d) 31.2 g/day

#4
In an experiment conducted to evaluate the Michaelis-Menten
constant, it was found that 1 g of bacteria could decompose the
waste at a maximum rate of 35 g/day when the waste
concentration was high. It was also found that the same
quantity of bacteria would decompose waste at a rate of 18
g/day when the waste concentration was 20 mg/L. Calculate
the rate of waste decomposition by 2 g of bacteria if the waste
concentration were maintained at 8 mg/L.
(a) 10.4 g/day
(b) 15.6 g/day
(c) 20.8 g/day
(d) 31.2 g/day
85
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#9
The enzymatic hydrolysis of an ester occurs according to the
following reaction:
enzymes
𝑅𝐶𝑂𝑂𝑅 ′ + 𝐻2𝑂 𝑅𝐶𝑂𝑂𝐻 + 𝑅 ′ 𝑂𝐻
The following data on the rate of formation of the ester at 25oC at
pH = 6.5 were obtained:
s (mM) 3.0 4.5 6.0 7.5 9.0 10.5
v (mM/s) 0.051 0.064 0.071 0.079 0.082 0.091
The Michaelis constant, Km, in mmol/L, is:

(a) 4.28
(b) 8.08
(c) 16.8
(d) 34.6

#9
The enzymatic hydrolysis of an ester occurs according to the
following reaction:
enzymes
𝑅𝐶𝑂𝑂𝑅 ′ + 𝐻2𝑂 𝑅𝐶𝑂𝑂𝐻 + 𝑅 ′ 𝑂𝐻
The following data on the rate of formation of the ester at 25oC at
pH = 6.5 were obtained:
s (mM) 3.0 4.5 6.0 7.5 9.0 10.5
v (mM/s) 0.051 0.064 0.071 0.079 0.082 0.091
The Michaelis constant, Km, in mmol/L, is:

(a) 4.28
(b) 8.08
(c) 16.8
(d) 34.6
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#17
There are several forms suggested by which the
hyperbolic Michaelis Menten equation may be
expressed linearly. If the substrate concentration, s, is
plotted against reaction velocity, v, a linear plot is
obtained. This equation is called:
(a) Lineweaver-Burk equation
(b) Eadie-Hofstee equation
(c) Hanes-Woolf equation
(d) Eisenthal-Cornish-Bowden equation

#17
There are several forms suggested by which the
hyperbolic Michaelis Menten equation may be
expressed linearly. If the substrate concentration, s, is
plotted against reaction velocity, v, a linear plot is
obtained. This equation is called:
(a) Lineweaver-Burk equation
(b) Eadie-Hofstee equation
(c) Hanes-Woolf equation
(d) Eisenthal-Cornish-Bowden equation
87
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#19
The enzyme in the stomach is:
(a) urease
(b) papase
(c) pepsin
(d) bromelis

#19
The enzyme in the stomach is:
(a) urease
(b) papase
(c) pepsin
(d) bromelis
88
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#39
It is defined as the quantity of enzymes needed to
transform 1.0 micromole of substrate to product per
minute at 30oC and optimal pH.
(a) International Unit
(b) Enzyme Unit
(c) Catalytic Unit
(d) all of these

#39
It is defined as the quantity of enzymes needed to
transform 1.0 micromole of substrate to product per
minute at 30oC and optimal pH.
(a) International Unit
(b) Enzyme Unit
(c) Catalytic Unit
(d) all of these
89
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#43
It states that there is a topographical, structural
compatibility between an enzyme and its substrate.
(a) lock-and-key theory
(b) Michaelis-Menten model
(c) Briggs-Haldane model
(d) compatibility theory

#43
It states that there is a topographical, structural
compatibility between an enzyme and its substrate.
(a) lock-and-key theory
(b) Michaelis-Menten model
(c) Briggs-Haldane model
(d) compatibility theory
90
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Bioreactor Design
Bioreactor Design
• There are three principal modes of bioreactor
operation:
• batch
• fed-batch
• continuous
• Characteristics such as final biomass, substrate, and
product concentrations can be determined for
different reactor operating schemes using mass
balances. (terms in kg/s or mol/s)
𝒅𝑴
= 𝑴𝒊 − 𝑴𝒐 + 𝑹 𝑮 − 𝑹 𝑪
𝒅𝒕
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Continuous Operations of
Mixed Reactors
• Bioreactors are
operated
continuously in
bioprocess industries
such as brewing,
production of bakers’
yeast, and waste
treatment.
• Enzyme conversions
can also be carried
out using continuous
systems.
Continuous Operations of
Mixed Reactors
• Well-mixed continuous reactors are often referred
to as continuous stirred tank reactors (CSTRs) or
continuous stirred tank fermenters (CSTFs).
• Different steady-state operation strategies are
available for CSTFs.
• chemostat – liquid volume is kept constant by setting
inlet and outlet flow rates equal; steady state is achieved
as concentrations in the chemostat adjust themselves to
the feed rate
• turbidostat – liquid volume also kept constant; inlet flow
rate is adjusted to keep biomass concentration constant
92
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Chemostats
Enzyme Reaction
• Apply a mass balance to the limiting substrate, s.
𝒅𝑴
= 𝑴𝒊 − 𝑴𝒐 + 𝑹𝑮 − 𝑹𝑪
𝒅𝒕
𝟎 = 𝑭𝒔𝒊 − 𝑭𝒔 − 𝑽
𝑲𝒎 + 𝒔
𝑫 𝒔𝒊 − 𝒔 =
𝑲𝒎 + 𝒔
Chemostats
Cell Culture
• Apply a mass balance to the biomass, x.
𝒅𝑴
= 𝑴𝒊 − 𝑴𝒐 + 𝑹 𝑮 − 𝑹 𝑪
𝒅𝒕
𝟎 = 𝑭𝒙𝒊 − 𝑭𝒙 + 𝝁𝒙𝑽 − 𝒌𝒅𝒆𝒂𝒕𝒉𝒙𝑽

Neglecting cell death,
𝝁𝒎𝒂𝒙𝒔
𝑫 𝒙 − 𝒙𝒊 = 𝒙
𝑲𝒔 + 𝒔
93
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#12
A continuously stirred tank reactor (CSTR) with a working volume of 15 m3
is used for the production of bakers’ yeast. The overall reaction for aerobic
fermentation is expressed as:
0.556 C6H12O6 + 0.301 NH3 + 1.43 O2 ⟶
0.301 C6H10O3N + 2.283 H2O + 1.532 CO2
The empirical formula for the biomass is C6H10O3N (44) and molasses
contains 40.8% w/v C6H12O6 (180).
Calculate the daily molasses consumption to maintain a daily production of
one metric ton if the residual sugar in the outgoing broth is 1.4 %w/v.
(a) 1465 L/day
(b) 2930 L/day
(c) 4395 L/day
(d) 5860 L/day

#12
0.556 C6H12O6 + 0.301 NH3 + 1.43 O2 ⟶
0.301 C6H10O3N + 2.283 H2O + 1.532 CO2
contains 40.8% w/v C6H12O6 (180).
Calculate the daily molasses consumption to maintain a daily production of
one metric ton if the residual sugar in the outgoing broth is 1.4 %w/v.
(a) 1465 L/day
(b) 2930 L/day
(c) 4395 L/day
(d) 5860 L/day
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#13
0.556 C6H12O6 + 0.301 NH3 + 1.43 O2 ⟶
0.301 C6H10O3N + 2.283 H2O + 1.532 CO2
contains 40.8% w/v C6H12O6 (180).
The specific growth rate of the yeast is:
(a) 0.13 /day
(b) 0.26 /day
(c) 0.39 /day
(d) 0.52 /day

#13
0.556 C6H12O6 + 0.301 NH3 + 1.43 O2 ⟶
0.301 C6H10O3N + 2.283 H2O + 1.532 CO2
contains 40.8% w/v C6H12O6 (180).
The specific growth rate of the yeast is:
(a) 0.13 /day
(b) 0.26 /day
(c) 0.39 /day
(d) 0.52 /day
95
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#16
It is desired to reduce the bacterial count of polluted water
from 30 million organisms per mL to 5 organisms per mL.
Calculate the number of completely mixed chlorine contact
chambers in series, each having a detention time of 120 min,
that would be required if the first order removal rate constant
is 2.6 h-1.
(a) 3 chambers
(b) 6 chambers
(c) 9 chambers
(d) 12 chambers

#16
It is desired to reduce the bacterial count of polluted water
from 30 million organisms per mL to 5 organisms per mL.
Calculate the number of completely mixed chlorine contact
chambers in series, each having a detention time of 120 min,
that would be required if the first order removal rate constant
is 2.6 h-1.
(a) 3 chambers
(b) 6 chambers
(c) 9 chambers
(d) 12 chambers
96
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Biochemical
Engineering
Engr. Peter Fowler
97

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Nucleotides and Nucleic Acids

Nucleotides and Nucleic Acids

Nucleotides and Nucleic Acids

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Amino Acids and Proteins

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C6H12O6 ⟶ 2CH3CH2OH + 2CO2

• Saturated fatty acids are highly flexible molecules.

• Most triglycerides contain two or three different

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