BIOLOGICAL BASICS OF

FERMENTATION INDUSTRIAL
ENGINEERING

CELLS
The major categories of life are the animal kingdom, the plant kingdom, and the
protist.

Cells are the structural and functional units of living organisms.

All cells share some structural features.
* Cell membrane: being selectively
permeable
* Cytoplasm: most of the enzymecatalyzed reactions of cell
metabolism occur
* Ribosomes: synthesis of proteins
* Nucleus (or nuclear body):
replication and storage of the
genetic material

 Cells must have very small

dimensions.
(1) Effective diffusion of nutrient
molecules
(2) Large ratio of the surface area
of cells to volume

There are two great classes of cells: prokaryotes and eucaryotes.

Prokaryotic: before the nucleus
The genetic material is localized in a rather irregular nuclear body or
nucleoid, which has no surrounding membrane.

Eukaryotic: well-formed nucleus

Comparison of prokaryotic and eukaryotic cells:

Prokaryotic Cells

Eukaryotic Cells

Size

0.25 m in diameter

Most are 1050 m in

diameter

Containment of DNA

Free in cytoplasm as
nucleoid

In nucleus, condensed with

proteins into multiple
chromosomes

Ploidy (number of
copies of the genetic
information)

Usually haploid ()

Almost always diploid ()

or polyploid

Mechanism of cell
replication

Simple division following

DNA replication

Mitosis () in somatic
cells (), meiosis (
) in gametes ()

Internal
compartmentation

No

Yes, with several different

kinds of organells

Glossary
Chromosomes (): structures that contain the nuclear DNA of a cell
Ribosomes (): intracellular structures composed of ribosomal RNA and
protein, the sites where protein synthesis occurs
Vacuole (,): a membrane-bound cavity within a cell that may function in
digestion, secretion (), storage, or excretion ()
Chloroplasts (): membrane-bound organelles of photosynthetic eucaryotes
where the biochemical conversion of light energy to ATP occurs; the sites of
photosynthesis in eukaryotic organisms
Nucleolus (): an RNA-rich intranuclear body not bounded by a limiting
membrane that is the site of ribosomal RNA synthesis in eucaryotes
Lysosomes (): an organelle containing hydrolytic enzymes involved in
autolytic and digestive processes
Golgi apparatus (): a membranous organelle of eukaryotic organisms
involved with the formation of secretory vesicles (,) and the synthesis of complex
polysaccharides
Mitochondria (): a semiautonomous () organelle found in
eukaryotic cells, the site of respiration and other cellular processes, consisting of an
outer membrane and an inner one that is convoluted ()
Respiration (): a mode of energy-yielding metabolism requiring a terminal
electron acceptor for substrate oxidation, with oxygen frequently used as the
terminal electron acceptor
Endoplasmic recticulum (): the extensive array of internal membranes in
a eukaryotic cell involved in coordinating protein synthesis

 The protist is further divided into two categories: procaryotes and eucaryotes.

* Bacteria are members of a group of diverse and ubiquitous prokaryotic, singlecelled organisms.
Bacteria occur in a variety of shapes: coccispherical or ovoid; bacilli
cylindrical or rod-shaped; spirillahelically coiled
* Actinomycetes are members of an order of bacteria in which species are
characterized by the formation of branching filaments and/or true filaments.
* Blue-green algae (cyanobacteria): prokaryotic, photosynthetic organisms
containing chlorophyll a, capable of evolving oxygen by the splitting of water.
* Fungi are a group of diverse and widespread unicellular and multicellular
eukaryotic organisms, lacking chlorophyll, usually bearing spores, and often
filamentous.
* Molds are a type of fungus having a filamentous structure.
* Yeasts are a category of fungi defined in terms of morphological and
physiological criteria, typically a unicellular, saprophytic organism that
characteristically ferments a range of carbohydrates and in which asexual
reproduction occurs by budding.
* Algae: a heterogeneous group of eukaryotic, photosynthetic, unicellular, and
multicellular organisms lacking true tissue differentiation.
* Protozoa: diverse, eukaryotic, typically unicellular nonphotosynthetic
microorganisms, generally lacking a rigid cell wall

 Microbial nomenclature follows the binomial system, for example, Bacillus

subtilis.
* The first word is the name of the genus and the second word is the species
name.
* The genus name is capitalized. When the same genus name is repeated several
times, it is abbreviated, for example, B. subtilis.
* The names are given in Latin or are Latinized; they are always italicized.
* The genus names have meanings:
Bacillus: a small rod; Lactobacillus: a small milk rod; Micrococcus: a small
grain; Clostridium: a small spindle; Pasteurella: after Louis Pasteur,
Latinized; Salmonella: after Daniel E. Salmon, Latinized; Saccharomyces:
sugar fungus.

BIOENERGETICS
Living organisms require energy for growth and maintenance.
The energy needs of all organisms are provided, directly or indirectly, by
solar energy.

Living organisms exchange energy and matter via the environment.

 Metabolic pathways are promoted by sequential enzyme systems.

* Linear pathway:

A E1 B E 2 C E 3 D E 4 E

* Circular or cyclic pathway:

Metabolism consists of catabolic (degradative) pathways and anabolic

(biosynthetic) pathways.

 Catabolic pathways converge to a few end products.

Biosynthetic (anabolic) pathways diverge to yield many products.

There are important differences between corresponding catabolic and anabolic

pathways.

In the cell, energy is trapped in organic compounds with high-energy bonds.

 Adenosine triphosphate (ATP) is one of the most important high-energy

compounds in cellular metabolism.

* Hydrolysis of ATP:
ATP + H2O ADP + HPO42

G = 7.3 kcal/mol

ADP + H2O AMP + HPO42

G = 7.3 kcal/mol

AMP + H2O Adenosine + HPO42

G = 3.4 kcal/mol

It is common for the terminal phosphate only to be involved in

reactions.
* Coupled reactions:
A+B C

G10 '

K1

C+D

K2

A+B+D

G20 '

E
K 3 K1 K 2

G30' G10 ' G20'

* Analog compounds of ATP, such as GTP, UTP and CTP, also store and transfer
high-energy phosphate bond, but not to the extent of ATP.

ELECTRON TRANSPORT
Electron-transferring reactions are oxidation-reduction reactions.

 Free-energy changes accompany electron transfers.

G 0' nFE0'

where n = number of electrons transferred

F = Faradays constant, 23.06 kcal mol1 volt1 or 96.5 kJ mol1 volt1
E0' = standard potential difference, volt
* Electron transport from NADH to O2:
NADH NAD+ + H+ + 2e

E0'

= +0.32 volt

1
2

E0'

= +0.82 volt

O2 + 2H + 2e H2O
+

NADH + H +
+

1
2

O2 NAD + H2O
+

E0'

= 1.14 volt

G = 2 96.5 1.14 = 220 kJ/mol

* Synthesis of ATP: ADP + Pi + H+ ATP + H2O G = 30.5 kJ/mol
How many moles of ATP are formed by oxidizing 1 mole of NADH or FADH2?

MAJOR METABOLIC PATHWAYS

Glycolysis
80% of the glucose used is broken down by glycolysis.

Overall equation:

Glucose + 2ADP + 2Pi + 2NAD+ 2 pyruvate + 2ATP + 2NADH

 Glycolysis has two phasesenergy investment phase and energy generation

phase.

 The Entner-Doudoroff pathwaya variation of glycolysis

Overall equation:
Glucose + ADP + Pi + NAD + NADP
2 pyruvate + ATP + NADH + NADPH

 Pyruvate follows different catabolic pathways depending on the organism and the
metabolic conditions.

Ethanol production: Zymomonas mobilis (bacteria) versus Saccharomyces uvarum

(yeast)

Citric Acid Cycle (or Tricarboxylic Acid Cycle)

Provide both the carbon skeletons needed as starting materials in biosynthesis
and the energy needed for the reactions.

Stoichiometry
Glycolysis: Glucose + 2ADP + 2Pi + 2NAD+ 2 pyruvate + 2ATP + 2NADH
Decarboxylation of pyruvate:
Pyruvate + NAD+ + CoA-SH acetyl-CoA + NADH + CO2
Citric acid cycle:
Acetyl-CoA + 3NAD+ + FAD + ADP + Pi
2CO2 + CoA-SH + 3NADH + 3H+ + FADH2 + ATP
Catabolism of glucose through glycolysis and citric acid cycle:
Glucose + 10NAD+ + 2FAD + 4ADP + 4Pi
6CO2 + 10NADH + 10H+ + 2FADH2 + 4ATP

[Problem] Yeast can grow both aerobically and anaerobically on glucose. When
yeast, which has been maintained under anaerobic conditions, is exposed to
oxygen, the rate of glucose consumption decreases. Why?
Anaerobically: energy production = 2ATP

Aerobically: energy production = 38ATP

The net result in the presence of O2 is a marked increase in the ATP/ADP ratio.
This inhibits phosphofructokinase and thus decreases the amount of glucose
utilized via glycolysis.

Glyoxalate Cycle
The glyoxalate cycle is a modification of the citric acid cycle.
In plants and microorganisms, the glyoxalate cycle converts fats to carbohydrates.
The biosynthetic capacity is absent in animals.

Overall reaction:
2 Acetyl-CoA + NAD+ + 2 H2O

succinate + 2 CoA-SH + NADH + 3H+

Pentose Phosphate Pathway

Serve four purposes: (1) production of NADPH, (2) synthesis of ribose
phosphate, (3) production of ATP, and (4) synthesis of glucose.

 The pentose phosphate pathway operates in two phasesoxidative and

nonoxidative.
(a) Oxidative phase: generation of reducing power as NADPH

(b) Nonoxidative phase: tailoring pentose phosphates to meet metabolic needs

 Balanced equations in pentose phosphate pathway:

* Generation of NADPH and ribose-5-phosphate
Glucose-6-phosphate + 2NADP+ ribose-5-phosphate + CO2 + 2NADPH + 2H+

* Conversion of pentose phosphate to six-carbon and three-carbon sugar

phosphates
3 Pentose-5-phosphate 2 fructose-6-phosphate + glyceraldehyde-3-phosphate

* Conversion of ribose-5-phosphate to glucose-6-phosphate

6 Ribose-5-phosphate +H2O 5 glucose-6-phosphate + Pi

* Complete oxidation of one mole of hexose phosphate to CO2

Hexose-6-phosphate + 12NADP+ 6CO2 + 12NADPH + 12H+ + Pi

Biosynthesis of Amino Acids

The biosynthesis of the 20 L-amino acids found in proteins represents the
formation of six families of related amino acids.
Transamination is the essential process for the synthesis of all of the amino
acids.

(1) -Ketoglutarate (in citric acid cycle)

glutamate glutamine, proline, arginine

(2) Oxaloacetate (in citric acid cycle)

aspartate asparagines, methionine, threonine ( isoleucine), lysine

(3) 3-Phosphoglycerate (in glycolysis) serine cysteine, glycine

(4) Pyruvate (in glycolysis) alanine, valine, leucine

(5) Phosphoenolpyruvate (in glycolysis) + erythrose 4-phosphate (in pentose

phosphate pathway) phenylalanine, tyrosine, tryptophan

(6) Ribose 5-phosphate (in pentose phosphate pathway) histidine

Catabolism of Amino Acids

The turnover of protein within cells is surprisingly rapid.
The halflifes of proteins vary from a few minutes to a few weeks.
Enable a cell to respond quickly to changing metabolic conditions.
Fates of amino acids released during protein turnover:
(1) Incorporated in new proteins
(2) Producing ATP
(3) Converted to carbohydrates or fatty acids
The first phase in the degradation of most amino acids is deamination.
* Transfer of -amino groups is catalyzed by transaminases.

Lipid Metabolism
Lipases can cleave the fatty acids from the glycerol portion of a triglyceride lipid
molecule.

Fatty acids are oxidized in two stages:

(1) -Oxidation to yield acetyl-CoA and ATP

Palmitoyl-S-CoA + 7CoA-SH + 35ADP + 35Pi + 7O2

8 acetyl-S-CoA + 35 ATP + 42H2O
(2) Oxidation of acetyl-CoA via the citric acid cycle
8 Acetyl-S-CoA + 96ADP + 96Pi + 16O2
16CO2 + 8CoA-SH + 96ATP + 104H2O

 Common reaction steps in the fatty acid oxidation cycle and citric acid cycle:

Cells often follow the same enzyme reaction pattern for bringing about
analogous metabolic reactions.
Acetyl-CoA has two possible fates:
(1) Being oxidized to CO2 via the citric acid cycle
(2) Being converted into ketone bodies to be circulated to the peripheral tissues

The metabolism of aliphatic

hydrocarbons is closely related to
fatty acid metabolism.

 Fatty acid biosynthesis is not a simple reversal of -oxidation.

The intermediates are bound to an acyl carrier protein (ACP or ACP-SH)
rather than to CoA.

Acetyl-CoA + 7 malonyl-CoA + 14NADPH + 20H+

CH3(CH2)14COO + 7CO2 + 8CoA-SH + 14NADP+ + 6H2O

A Summary of Metabolic Pathways

* Metabolic reactions can be classified in three major categories: fueling

reactions, biosynthesis reactions, and polymerization reactions.