CHE323

Biochemical Engineering 1

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 Definitions
• Biochemical Engineering involves the application of chemical engineering principles and
approaches to biological based systems and processes.
-It is central to the areas of environmental engineering, and to biotechnology processes
that produce pharmaceuticals, fine chemicals and genetically engineered products.
-Study of the biological and biochemical principles supports the field of biochemical
engineering.
-A Biochemical Engineer is someone who when with engineers, talks biology, when with
biologists, talks engineering and when with biochemical engineers, talk politics.
• Bioprocessing is any process in which microbes or living organisms or enzymes play a vital role
in getting transformation of the feed into useful products.
-Examples are converting milk to curds, fruit juices into wines, sugars into alcohols.
-It’s a branch of chemical/process engineering dealing with design and development of
equipment and processes that use biological components such as enzymes or
microorganisms
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 Biochemical Engineering is a multidisciplinary field:

Material science
Chemical engineering

Biology:
microbiology,
molecular biology
Biochemical
Engineering
Pharmacology
Biochemistry

Chemistry Genetics

Medicine

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 See Table in the lecture note
for some stages of development
in bioprocessing (fermentation)

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 Related disciplines/areas of specialization
• Metabolic engineering including metabolic modeling, bioprocess
engineering, process control, bio-separation, bio-informatics, bio-material
engineering, tissue engineering, manufacture engineer, reactor design.
• Biochemical engineering covers research at the scale of the biocatalyst
development (microbe, insect cell, mammalian cell, plant cell, enzyme)
• Biotechnology is a study about biological systems or living organisms to
make or modify products or processes for specific use, such as in agriculture,
food production, and medicine.

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Traditional and modern application of biotechnology
• They are in the areas of food, bakery products and alcoholic
beverages.
• Earliest application was in the production of wine from fruit juices.
• Areas of health and hygiene for the production of vaccines, enzymes,
various fermented foods, organic acids etc.
• Bio-processing or biotechnology operations are interrelated with a
large number of faculties in science.
• Alcoholic fermentation was considered to involve both chemical and
microorganisms.
• The biochemical engineers were considered to provide sterile
environments in most bio-processing.
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 Unit operations in bioprocesses
The whole bio-processing operations can be broadly classified into two
classes/types of operations.
 Fermentation
 Product recovery and effluent treatment.
• Fermentation is biochemical operation and can be classified as unit process.
• Operations carried out on the fermentation broth for product recovery and
downstream operations including effluent treatment may be classified as unit
operation.
• Some of the operations carried out on the fermenter such as fluid dynamics,
mixing, air sparging, heat transfer to the fluids may also be categorized as unit
operations

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• Product recovery and downstream processing lines involve mixing and separations of
various phases, streams and fluids.
We can broadly comprehend the systems encountered as
 Solid-liquid
 Liquid-liquid
 Liquid-liquid-solid
 Liquid-gas
 Solid-liquid-gas
 Solid-solid
Mixing is also one of the most important unit operations in bio-processing. It could be for
• G-L, L-L, L-S, G-L-S systems.
• Design of various impellers/mixers for mixing is a challenge for biochemical engineer.
• Efficient mixing of the broth decides the progress of reaction.
- for example, mixing of gas in a fermentation broth is useful for the utilization of microbial
cells to respire, grow, increase in size/multiply, and perform well.

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Outline of integrated bioprocess
Integrated bio-processing consists of various steps:

Step 1: Isolation of the strain

• Identification and isolation of the microorganism which brings out
the desired bioconversion.
-This is generally the task of a microbiologist.
-It involves some shake flask experimentation, etc.
• The techno-economic viability of the process will be taken up
subsequently if the results of this step 1 are encouraging.

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Step 2: Preservation of the strain
• The strain isolated in step 1 will be preserved for future use.
• Its ability to perform and yield the products should also be preserved.
The strain can therefore be stored ;
a) Refrigerated temperature (2 – 6 oC)
b) At frozen storage temperature (-18 to -80 oC)
c) By freeze drying (lyophilization)

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 Step 3: Growth of inoculums
• Before using the strain in a fermenter/bioreactor, the inoculum (cells
added) is cultured
for growth.
• The preserved strain/culture is revived by growth in shake flasks or by
solid-state fermentation on the solid surfaces.
• Solid state fermentation(SSF) is a method of growing microorganisms in an
environment of limited moisture without having free flow of water.
-In other words, microorganisms grow on a solid surface which is moisten
bed and which has also got free access to air.

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Step 4: Pre-fermentation culturing
• Before the cells are admitted into the fermenter for performing
bioconversion, they are initially grown separately with nutrients and the
substrate so that the cells can multiply and proliferate.
• This will help increase the cell density. The optimal cell concentrations in a
fermenter are as follows:
1) Bacterial: 0.1 – 3.0%
2) Actinomycetes: 5 – 10%
3) Fungi: 5 – 10%

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Step 5: Fermentation
• Major activity in industrial operation in the whole bioprocess is FERMENTATION.
• Fermentation is the heart of the bio-processing operation.
• Fermenter sizes vary from 1 to 450 m3, depending upon the type of
fermentation process.
Based on capacity, tonnage and nature of the
fermentation product, fermenters can be
classified;
1. Batch fermenter.
2. Fed-batch fermenter.
3. Continuous fermenter.
The conditions could be aerobic (with bubbling
of air) or anaerobic (in the absence of air).

A Fermenter
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Step 6: Recovery and purification of the product
• Recovery and purification sometimes decide the economic viability of the
process.
• The cost of recovery can vary anywhere between 20 and 60% of the total
manufacturing costs.
The methodology depends on;
-Nature of the cells.
How to hold the products : is it intracellular (product is held within the cells) or
extracellular (the product is excreted from the cells).
-Solids can be removed by simple filtration or centrifugation techniques.
-The intracellular material is obtained by cell disruption techniques for example
intracellular enzyme extraction
-Purification and isolation of the final products are carried out using different
unit operations.
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Step 7: Treatment of effluents
• Effluents are released during fermentation processes.
• The effluents may be rich in organic matter and may be a potential hazard for
the environment if released like that.
• Ability to economically be able to treat effluents before release to the
environment makes or mars the viability of the product manufacture.
• Various effluent-treatment techniques can be classified as:
-Physical
-Chemical
-Biological
• The final choice depends upon the individual cases and local
circumstances.

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 A process for converting biomass to ethanol
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 Microbiology
• Microbiology is the study of microorganism which are not only microscopic and exist as
single cells, but also ultramicroscopic organism which are not cellular and hence cannot exist
independently e.g. viruses
-It deals with study of functioning of cells, their diversity and evolution, their interaction
with environment, other living organism and man.
• Microbiology forms the basis for the complimentary development in cell biology,
biochemistry, molecular biology and genetics.
• Microbiology has evolved as an important branch of science, and is studied with respect to 2
major aspects:
-As basic biological science by providing a system to understand the nature of life
processes, the principle behind it, and the genetics which is involved
-As applied biological science, microbiology deals with the study of useful
microorganisms as well as that of pathogenic organisms.
***See the lecture notes for different past discoveries
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 Introduction to Microbiology
Branches of Microbiology
1. Medical microbiology
• Study of pathogenic (disease causing) organisms and ways to eliminate them. Common diseases such
as typhoid fever, tuberculosis (bacterial), hepatitis C (viral), malaria (parasitic), dandruff, candida
(fungal infections)
2. Agricultural microbiology
• Study of plant disease, understanding beneficial interactions with plant systems, like soil fertility, crop
protection, and increasing yield.
3. Environmental microbiology
• Study of the relationship of microorganisms with its habitat, pollution effect, and its impact on
environment from the stand point of ecological balance and health
4. Food & Dairy microbiology
• Study of microorganisms that produce various food and dairy products; study of control of
microorganisms in food and transmission of food-borne diseases.
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 Microscopy
• Microscopy is an important tool for revealing the secrets of the world of
small creatures.
• Microorganisms and their structural components are measured in smaller
units such as micrometers or microns (10-6 m), nanometers or millimicrons
(10-9 m), and angstroms (10-10 m).
• Microscopic resolutions are limited by the size/type of the microbe. Some
microbes are unicellular, algae, fungi, protozoa, viruses, proteins, lipids, small
molecule.
• Operation ranges could vary from unaided eye, to light microscope, and to
electron microscope.

***see the lecture notes for different ranges of microscopic resolutions

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 Microbial taxonomy
• Taxonomy is the subject of classification of biological existence of life species.
• Earlier, all living organisms were classified under two main kingdoms, namely, Plantae and
Animalia by Swedish botanist Carolus Linnaeus in the 18th century.
• In 1969, Robert H. Whittaker proposed a 5-kingdom classification:
1. Monera
2. Protista
3. Fungi
4. Plantae
1. Animalia
A term for generalizing the taxonomical classification of microorganisms is UNIVERSAL
ANCESTOR which can also be referred to as Universal Phylogenetic Tree (see next slide).
It is referred to as Last Universal Common Ancestor (LUCA), it’s the most recent population of
organisms from which all organisms now living on earth have common descent

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***see the lecture notes for the simplified classification of universal ancestor

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Monera: true bacteria and blue green algae.
Prostita: eucaryotes such as protozoa which are unicellular, contains chlorophyll
(plant like) and possess movement (animal like).
Fungi: include non-green eucaryotic organisms like slime moulds, bread moulds,
sac fungi.
-Composition of their cell wall differed from that of plants, and had adjacent
cells without separation, hence are not considered as true multicellular
organism
Plantae: include algae, all mosses, ferns, cornifers, and flowering plants.
Animalia: Sponges (are primitive multicellular animals, incapable of moving),
worms, insects, and vertebrates

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Microbial diversity
• Evolution roots of cell form a basis for understanding the microbial
diversity.
• Microbial diversity can be seen in terms of variations:
-in cell size,
-morphology (internal structure),
-metabolism (chemical reactions in the body's cells that change
food into energy),
-adaptation (adjusting or changing to become more suited to an
environment),
-growth (increase in size or concentration) etc.

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 Microbial Nomenclature
• Basic taxonomic unit is species which can be defined as a collection of similar
strains.
• Groups of species are collected as genera. They share major properties.
• Groups are classified into families, families into order, and orders into divisions.
Following the binomial system of nomenclature, microorganisms are given genius
and species name, which are either Latin or Greek derivations.
Example;
• Bacillus subtilius or Bacillus meaning “rod shape”, which indicates its slender nature;
• B. cereus meaning “waxen”(shape can easily change);
• B. stearothermophilus meaning “heat loving”;
• B. acidoceldarius meaning “acid-thermal”
They are written in italics with the genus name stating with capital letter and the species name
with a small letter.
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There are many ways of grouping (classification) of procaryotes.
• The characteristics of taxonomic approach include morphology,
-Gram reaction (Gram reaction is a classical technique to identify the basic difference in
the cell wall structure of the bacteria.
-The cells are stained with crystal violet dye, and then treated with iodine solution,
and then cells washed with alcohol.
• Those which retain the blue crystal violet colour are classified as gram positive, and
those which do not retain the colour are called as gram negative species),
• Other approaches for group classifications are:
 nutrition, cell wall chemistry, pigment, storage products, ability to use various substrates,
fermentation products, gaseous needs, temperature, pH requirement, tolerances, sensitivity.

Molecular taxonomy includes guanine and cytosine ratio (GC ratio) in organisms, the extent of
DNA: DNA hybridization, amino acid sequencing and protein analysis.

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 Chemical composition
• Cells are composed of small molecules as well as macromolecules.
• They are made up of 4 basic elements, viz. Carbon, Oxygen, Hydrogen and
Nitrogen.
-Phosphorus, Iron, Sulphur, Zinc, Manganese, Copper, Molybdenum, and Cobalt
are also present apart from the 4 basic elements.
• Water accounts for 90% of the weight of the cells.
• Of the macromolecules, proteins are most abundant by weight (55%).
• Most procaryotes require an organic compound of some sort as their source of
carbon.
• After carbon, the most abundant element in cell is nitrogen (12% by dry
weight), which is a major constituent of protein and nucleic acids.
• Nitrogen is found in organic and inorganic forms, and is mostly assimilated as
ammonia NH3, nitrates NO3 or N2.
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• Organisms assimilate various organic compounds, and use them to make new cell wall
materials, which may be amino acids, fatty acids, organic acids, sugars, nitrogen bases
and aromatic compounds.
• Macronutrients required in nature and media for organisms include Carbon, Hydrogen,
Oxygen, Nitrogen, phosphorus, Sulphur, Potassium, Magnesium, Sodium, Calcium, Iron.
• Micronutrients required by cells include; Chromium, Cobalt, Copper, Manganese,
Molybdenum, Nickel, Selenium, Tungsten, Vanadium, Zinc, Iron.
• GROWTH FACTORS
-They are the organic compounds required in small amounts for growth and
metabolism, and these include vitamins, amino acids, purines, pyrimidines.
-Vitamins are not only needed for growth, but also play an important role as co-
enzymes. Most of the vitamins are synthesized by organisms themselves, but some
depends on external sources.
***see the lecture notes for more macronutrients and the chemical forms in which they are
supplied.

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 Module 3: Prokaryotes and Eukaryotes
Cells have evolved two architectural plans;
1. Procaryotes : cells without a nucleus.
2. Eucaryotes: cells with a nucleus.

THE PROCARYOTE
• In Greek means primitive nucleus. Includes Bacteria and Archaea.
• Genetic material is not enclosed within membrane.
• Lack membrane-bound organelles,.
• Cell walls contain complex polysaccharide peptidoglycan (a polymer
consisting of sugars and amino acids that forms a mesh-like layer
outside the plasma membrane).

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• They have a simple method of reproduction.
• Procaryotes include a vast heterogeneous group of very small
unicellular organisms which comprise eubacteria and
archaebacteria.
• Most range from 0.5 to 3 µm in diameter and 2-8 µm in length.
• They have a volume of 10-12 ml per cell and may weigh approximately
10-12 g per cell.
• Variously shaped like cocci, spherical to oval, streptococci, as tetrads,
rod-shaped bacillus etc.

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 Procaryotic cell

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• They have external appendages (secondary supports) as glycocalyx, flagella,
prokaryotic flagellum, axial filaments, fimbriae, pili.
• Bacterial cell wall is complex, semi-rigid and is responsible for characteristic
shape.
• The cell wall protects cell organelles from external environment and helps in
anchorage.
• The cell wall is credited for classification of major types of bacteria.
• Some primitive groups do not possess at all or possess a very little cell wall
material, e.g. mycoplasm which are smallest bacteria.

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 Cell wall: A rigid wall surrounding the cell, which approximately measures
200 Angstron unit.
Cell membrane: It is present just inner to the cell wall and has about 70
Angstron unit. It is also called plasma membrane. The cell membrane plays a
vital role in controlling the ingress (entering or going in) and egress (leaving
or going out).
Nuclear zone: It is large, ill-defined structure. It acts as dominant control
centre for the cell operation.
Ribosomes: They are grainy dark sports inside the cells. They function as the
sites for biochemical reactions. They are also called the sites of protein
synthesis
Cytoplasm: This is a fluid material occupying the rest of the space in the cell
(See diagram in the lecture note)

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 Eukaryotes (true nucleus)
eu = good or well, karyon = nucleus
• Consist of three main components: cell membrane, cytoplasm, nucleus.
• The cells are larger and more complex than the prokaryotic cells.
• They have the generic material enclosed in a specialized membrane.
• They contain distinct structures called cell organelles within the cytoplasm (see diagram).
• Typical eucaryotic cells range from 2 to 200 µm in diameter.
• They are characterized by the presence of definitely organized nucleus
• There is the presence of nuclear membrane and nucleolus, well organized cytoplasmic
organelles like mitochondria, plastids, ribosomes, endoplasmic reticulum, lysosomes, golgi
body etc.
• Examples are algae (except blue algae) and all other higher animals and plant cells.
NOTE that structures of eukaryotic cell, plants and animal differ.

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Eukaryotic cell (animal)
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Eukaryotic cell (Plant)
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 Plasma membrane
• This is also called ‘’unit membrane’’ and the nature of this outer covering depends on the
particular cell.
• Cells of higher animals have a thin cell coat.
• It possesses adhesive properties thus binding the like cells to form specialized tissues and
organs.
Endoplasmic reticulum (ER)
• It’s a complex membrane leading from the cell membrane into the cell and extends
throughout the cytoplasm.
• It is present in two forms: Rough ER which is covered with dark granules called ribosomes
and the smooth ER which is free from the dark granules.
• The function of ER is to synthesize lipids like triacylglycerides, phospholipids, sterols, etc.
Nucleus
• The largest cellular organelle that is surrounded by a double-layered nuclear envelope.
• The outer layer is continuous with the membrane of endoplasmic reticulum
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• The two nuclear membranes or the nuclear pores (membrane is porous) have a diameter of
90 nm.
• The nucleus is composed of DNA, thus acting as the repository of genetic material.
• It is the control centre of the cell, controlling the catalytic activity at the ribosomes.
Ribosomes
• These are the sites for the biochemical reactions and much of the ribosomes are embedded
in the surface of the ER.
• The major function of the ribosomes is to synthesize proteins
• They are also called the sites of protein synthesis.
Mitochondria
• These are rod-like or filamentous structures occupying 1/5th of the total cell volume.
• It measures 1.0 x 3.0 micrometer.
• Its major function is to catalyse the reactions and produce enormous amount of energy in
the form of ATP (adenosine triphosphate). They are therefore known as the power houses of
the cell.
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 Vacuoles, Golgi complex, lysosomes
• These are the remaining organelles that in general serve to isolate chemical reactions or
chemical compounds from the cytoplasm.
(A simple illustration of the eukaryotic animal cell structure is provided in the lecture note)

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 Differences between prokaryotes
and eukaryotes

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VIRUSES
• They are not classified as a part of any 5-kingdom.
• There are no orders, divisions and kingdoms established for viruses.
• They lack formal names, and most of them acquired their names from source
e.g. measles virus derive its name after the disease; Coxsackie virus after the
place Coxsackie, New Tork, where it was originally isolated, ebola virus derived
its name from the town it was first discovered, HIV-AIDS (human
immunodeficiency virus-acquired immunodeficiency syndrome), coronavirus,
etc.
• Viruses are categorized into genera, and each genus name ends with a suffix.
• Virus and genera have been organized into families each ending with –viridae.
• Viruses are not composed of cells, and use anabolic machinery within living
host cells to multiply.
• A virus genome (set of chromosomes) can direct biosynthesis inside a host
cell, and can get incorporated into host genome.
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 Virus

Fungi
Yeast

Algae

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Fungi
• They are a diverse group of eucaryotes lacking chlorophyll and are filamentous,
with the cell wall made up of chitin and coenocytic (i.e. cytoplasm mingles
between adjacent walls through pores).
• They are typically aerobic, found in damp and dark places.
• They are active producers of various hydrolytic enzymes, and hence they can
decompose cellulose and lignin (like paper and wood products).
• They can also grow on the surface of electrical insulators and make them
transmit electricity.
• They are mostly saprophytic (live and feed on dead and decaying organisms)
with complex life cycles involving spore formation.

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They are mainly classified into;
1) moulds
2) Yeasts
Yeasts are capable of anaerobic growth and survive in different environments. If access is given
to oxygen, yeasts perform aerobic respiration to metabolize carbohydrates to CO2 and H2O.
• In the absence of oxygen, they ferment carbohydrates to ethanol and CO2; hence they are
used in brewing, wine making and baking industries.
ALGAE
• They are eucaryotic, photosynthetic, multicellular, non-motile.
• More similar to plants, i.e. have branching structures (leaf).
• Are attached to substrates by root-like hold fast.
• Some contain pigments (photosynthetic)
• Cell organisation, process of photosynthesis and storage materials link them strongly to
higher plants.
• Their mode of nutrition in some cases is non-photosynthetic.
• Reproduction have resemblance close to animals.
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• They are considered as primary food producers as they convert chemically
simple nutrients to complex organic matter.
• Their dead cells contribute to the formation of a complex organic material called
“humus” which is provided as food to other microbes.
Protozoans
• It means “first animals”
• Except the flagellate algae, the phylum protozoa are the only animal group in
the entire kingdom of Protista.
• They are heterogeneous group with highly specialized cell structure, mode of
life and reproduction.
• They produce asexually by cell fission or by genetic combination and
multiplication. This results in rejuvenation of an asexual process called
“Conjugation”

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Paramecium
Euglena

Amoeba PROTOZOANS

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• All protozoa are chemoorganotrophic, capable of taking solid particles into cell.
• They respond to stimuli such as heat, chemicals, gravity and electricity.
• Certain organisms even have eye spot which can distinguish light of different wavelength.

Summary
• Cell structure, metabolism and function of the cell constitute the core of microbiology.
• Biochemical Engineering is the application of these core microbiology area to make
economically useful metabolic products.
• The understanding of these subjects and ability to interweave them with process
engineering skills can lead to design of bioreactors which make the cells to produce
useful metabolic products from organic substrates.
• Successful production and economization of a fermentation process requires both
industrial microbiologist as well as a biochemical engineer along with constant
experimental work and patience.

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 Module 4

Introduction to Biochemistry

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• It is the study of life cyclic processes in terms of chemicals.
• It is not the study of chemistry of living organisms.
• It obtains information from the basic microorganisms viz., bacteria,
viruses, algae and fungi.
• It draws information on energetics from basic thermodynamics.
• Some of the chemical/biochemical reactions in the living
organisms are facilitated by another type of compounds known as
enzymes. This facilitation is known as catalysis.
• Enzymes are therefore known as biocatalysts or biological
catalysts.
• Cells themselves contain some of the enzymes.
• Cells regulate the type of enzyme and its number by which it
regulates both the type of biochemical reaction and its rate.
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• Genetic engineering deals with the information flow of the living organisms.
• Biochemistry, coupled with genetic engineering principles play a vital role in
devising techniques for manipulating most of the biochemical transformations.
• Living organisms contain various biomolecules which are the building blocks of
the cell and also help in storing and releasing energy for bio-transformations.
• Biomolecules include carbohydrates, lipids, proteins, nucleic acids, vitamins, etc.

 In the following slides, we shall discuss briefly the various biomolecules, their
structural formulae and the functions performed by them.
 Detailed discussions on each one are available in any standard book of
biochemistry.

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 Lipids
• Classified as compounds which are fatty/oily in nature and present in cells and
tissues.
• Are insoluble in water.
• Are soluble in non-polar solvents like n-hexane, chloroform, benzene, etc., hence
can be extracted from the organisms using these solvents.
• They release a lot of energy on break down and hence are considered as the
energy storage media.
• They contain a large proportion of C-H bonds.
• Upon saponification, they release fatty acids and glycerol, and hence glycerol is
considered as a binding agent for fatty acids.
• They are synthesized by the cells from sugars.
• Lipids such as vitamins and hormones have intense biological activity.
• They are grouped based on their chemical composition.
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• They can be combined with other classes of compounds and are
known as;
-lipoproteins,
-proteolipids,
-phosphatidopeptides,
-lipoaminoacids, and
-lipopolysaccharides.
• Some lipids contain glycerol [e.g neutral fats, phospholipids
(phosphatides, phosphoglycerides & phosphoinositides)],
• while some do not contain glycerol [e.g. Sphingolipids (ceramides,
Sphingomyelins)], aliphatic alcohols and waxes (terpenes, steroids).

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• As biomolecules, they are a constituent of cell walls and form a protective
coating to the cell.
• They encourage some species-specific reactions.
• They are energy carriers, and release the energy as and when the cell requires
it.

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 Fatty acids
•  Lipids are a broader class of molecules and fatty acids are a part of it. 
• Fatty acids are either saturated or unsaturated while lipids are polymers
of fatty acids with a nonpolar hydrocarbon chain and a small polar oxygen
group.
• Fatty acids are generally available in the esterified (combination with an
alcohol or an acid, to form an ester) form in cells and tissues, and are rarely
available in free form.
• Ester is a chemical compound derived from an acid (organic or inorganic) in
which at least one –OH group is replaced by an –O– group (a substitution
reaction)
• They are named on the basis of the hydrocarbon from which they are
derived.
• The hydrocarbons may be saturated or unsaturated.
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 55
• In saturated fatty acids, the carbon atoms hold as many hydrogen
atoms as possible in addition to the carboxylic grouping.
• In the unsaturated fatty acid, the carbon atoms hold double and triple
bonds.
• Fatty acids differ from each other primarily in chain length and in the
number and position of their unsaturated bonds.
• Fatty acid esters of glycerol are called acyl-glycerols or glycerides

(See some formulas and structures of lipids in the lecture note)

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 56

 Amino acids & Proteins
•
Amino acids are the building blocks of proteins.
• They are 20 amino acids present in all living organisms.
• These 20 amino acids have different structural configurations and are
represented by three lettered symbol (e.g. Alanin, Ala, one letter symbol A).
• They are organized into primary, secondary, tertiary, and quaternary structures.
• All enzymes are proteins and they catalyze biochemical reactions as
biocatalysts.
• The amino acids are linked through peptide linkage (see lecture note).
• Note that as many as 300 amino acids occur in nature of which only 20 are
known.
(Place the structures of Alanine, Leucine, and Threonine here)

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 57

• They are isolated from plants, animals and microbes.
• The functional groups amino (–NH2) is basic while the carboxyl (-COOH) is
acidic, there are some neutral amino acids.
• The R’s is different for different amino acids.
• Both amino and carboxyl groups are attached to the same carbon atom.
• If the number of both functional groups present are the same, it is known as
neutral amino acid.
• Amino acids exhibit the optical isomerism as Laevo and Dextro amino acids.
(place the 2 structures here)

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 58

 Properties of amino acids
Amino acids differ in physical as well as chemical properties which ultimately
determine the characteristics of the proteins.
Physical
1. Most are soluble in water and insoluble in organic solvents.
2. Proteins generally melt at higher temperatures, at temperatures greater than
200 oC.
3. Amino acids can be sweet like glycerine, alanine, valine etc. They can be
tasteless as leucine or be bitter as arginine, isoleucine etc.
4. They have both acidic and basic groups, they can donate or accept protons.
Hence are called ampholytes.
5. Each amino acid has a characteristic pH at which it caries both positive and
negative charges and exist as a zwitterion.

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 59

• Isoelectric pH: This is the pH at which a molecule exists as a zwitterion or the
dipolar ion and carries no net charge. Thus, the molecule is electrically neutral.
Chemical
1. Form salts with base (-COONa)
2. They form esters (-COOR’)
3. In Biuret solution: A dilute solution of copper sulphate when added to a
protein solution mixed with sodium hydroxide, a violet colour appears.
4. Violet colour is due to the formation of a coordination compound between Cu2+
and COO and –NH– groups of the peptide chain.

(Study the 20 amino acids from Alanine (No. 1) to Valine (No. 20).

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 Proteins
• Derived from the Greek word proteios which means “primary”.
• They are considered to be the beginners and builders of biochemical reaction.
• They occupy a central position in the construction and functioning of living
matter
• Most abundant organic molecules of the living system.
• Occur in every part of the cell and constitute about 50% of the cellular dry
weight.
• All enzymes are proteins and they catalyze biochemical reactions as biocatalyst.
• Collagen is an elongated protein which is responsible for the tensile strength of
skin and bones
• They help in the transport of oxygen into blood, and transmission of nerve
impulses.
• Proteins constitute a major part of the animal tissue
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 61
 Functions of Proteins
1. Static functions
• Responsible for the structure and strength of the body. For example, collagen
and elastin are found in bone matrix, vascular system and alpha keratin in the
epidermal tissues.
2. Dynamic functions
• They act as enzymes, hormones, blood clotting factors, immunoglobulins,
membrane receptors.
• The proteins and their expressions represent the functional form of DNA
information.

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 Classification of proteins
1. Functional
• Structural proteins: keratin of hair, nails, and collagens of
bones.
• Enzymes or catalytic: Hexokinase, pepsin etc.
• Hormonal : Insulin, growth hormones
• Storage: Ovalbumin
• Defense: Snake venom, immunoglobulin
• Receptor: For hormones, viruses

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 2. Chemical nature and solubility
(put the protein organizations here)

Simple proteins
Made of chains of amino acid units only joined by peptide linkage.
On hydrolysis, these yield mixtures of amino acids and nothing else.
Conjugated
Made up of simple protein united covalently or non-covalently with a non-protein
part called PROSTHETIC GROUP or CO-FACTOR.
Derived
They are obtained as degradation products due to the hydrolysis of proteins with
acids, alkalis or enzymes.

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 3.Nutritional classification
Based on the composition of the essential amino acids, proteins are classified as
Complete proteins
• Have all the ten essential amino acids in the required proportions.
• Are required for growth e,g. egg albumin, milk casein.
Partially incomplete
• They partially lack one or more of the essential amino acids.
• They are required for growth, e.g, wheat and rice proteins.
Incomplete Proteins
• They totally lack one or more of the essential amino acids for example gelatin,
maize proteins etc.
• Proteins are the polymers of L-alpha amino acids. The complete hydrolysis with
the Conc. HCl for several hours yields L-alpha amino acids.
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 65
Protein structures
• The simplest condensation between 2 amino acids to form one molecule yields
a dipeptide.
• Polypeptides are large molecules of amino acids linked together via peptide
bonds.

(Dipeptide bond structure)

• The structure of proteins has various levels as primary, secondary, tertiary and
quartenary.

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 66

Primary structure
• The sequence is linked by peptide forms of polypeptide.
• The structure is important genetically because it indirectly suggests the sequence of
nucleotides in DNA.
• It is important structurally because the primary structures form the basis of higher levels of
organisation of protein structure.

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 67

Phe Val Asn
Gln leu
Gln Glu Val
Cys
S S
Ala Ser
Protein primary structure

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Secondary Structure
The secondary structure of protein arises from the way primary structure is
folded, maximizing the number of hydrogen bonds.
This structure has effect of lowering the free energy because of the folding and
hydrogen bond which make interaction with water possible.

(Place the secondary structure of protein here)

Tertiary structure
A polypeptide chain with its secondary structure may be further folded and
twisted about itself precisely because of the variety of amino acid present and
the different chemical properties of R-groups.

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Hydrogen bonding Ball & stick structure
structure

Secondary protein structure could be α-helix structure or β-pleated sheet

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 70

Tertiary protein structure

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 Quaternary structure
• This is the level of organization concerned with sub-unit interactions and
assembly.
• It applies therefore only to multimeric proteins, i.e. proteins made up of more
than one sub-unit.
• The polypeptides (which are multimeric) are quaternary in structure.
• Quaternary is a four fold structure.
• Polypeptide which are quaternary can have identical polypeptides or several
different kinds of polypeptides altogether forming a quarternary, e.g.
Haemoglobin.

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06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 74
Protein Denaturation & Renaturation

(Place the Diagram here)

• Protein in their functional confirmation are called native proteins.

• A specific protein is important for biological function.
• The loss of three dimensional structure of protein is termed DENATURATION.
• This can be caused by heat, extreme pH, certain miscible organic solvents such
as alcohol or acetone, and solute like urea, detergents are all known to
denature proteins.
• After a protein has been denatured by exposure to an adverse environment, it
will often return to native, biologically active conformation following the
restoration of suitable conditions.

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• It means that the 1o structure determines secondary and tertiary structures.
• Proteins in which the structural stabilizing bonds have been ruptured are said to
be denatured.
• An example is the boiling of egg. After boiling, heat denatures the egg albumin
and the various yolk proteins. Its usually impossible to revert the process.
However, some proteins can be denatured reversibly, e.g., the enzymes
ribonuclease.
• When a denatured protein snaps back to its original tertiary structure exhibiting
catalytic activity, we call this the re-naturation of proteins.

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 Carbohydrates
• Are also referred to as saccharides.
• Are large group of compounds which are poly-hydroxyaldehydes or poly-
hydroxyketones and their derivatives.
• They contain carbon, hydrogen and oxygen, with the ratio of hydrogen and
oxygen being 2:1.
• Have general chemical formula Cx(H2O)y
• May be classified as monosaccharides, oligosaccharides (di- and tri-
saccharides), polysaccharides, high molecular weight poly-saccharides.

(Place structures here)

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Monosaccharides are named based on the numbers of carbon atoms:
3-trioses, e.g glyceraldehyde;
4-tetroses, e.g erythrose;
5-pentoses, e.g arabinose, xylose, ribose, rhamnose;
6-hexoses, e.g. glucose, galactose, fructose, mannose;

Disaccaharides are anhydrides of two monosaccharides, which include sucrose,

maltose, lactose, and cellobiose.

Oligosaccharides are anhydrides of several monosaccharides residues.

Compounds containing ten or less monosaccharides units are called
oligosaccharides while those containing more than ten are called polysaccharides.
Polysaccharides include starches, cellulose. They are also known as glycans.

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• Polysaccharides are anhydrides of one or more monosaccharides in
which a large number of units are combined.
• Starches are nutritional reservoir in plants corresponding alpha(1,4)
linkages.
• The repeating disaccharide unit in starch is maltose.
• Native starches are a mixture of two compounds, viz, amylose and
amylopectin.
Cellulose is the compound which gives strength to plant tissues.
• Acid hydrolysis of cellulose yields glucose of about 95-96%.
• Glucose units are joined in beta(1,4)linkages.
• The purest form being cotton containing at least 90% pure cellulose.

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06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 81
VITAMINS
• They are group of organic compounds required in trace amounts to stimulate
body growth.
• They also keep away certain types of diseases.
• They are also present in certain enzymes to assist them in their catalytic
activity. Hence they are also known as co-enzymes.
• They are present in living cells in addition to lipids, proteins, carbohydrates,
nucleic acids, etc.
• Most vitamins contain amines, some do not contain amine but the name
Vitamin is retained.
• Vitamins are classified into two groups as water soluble and fat soluble.
Examples include Ascorbic acid (Vit-C), Folic acid, Biotin, Riboflavin (Vit-B2),
Thiamin (B1), Nicotinic acid (niacin), Vitamin A, D, E, K, Inositol.
(Check the structures of some of these vitamins)
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 82
REVIEW QUESTIONS
• Describe water soluble and fat-soluble vitamins.
• Write short notes on biomolecules.
• What are steroids, terpenes, saturated and unsaturated fatty acids.

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DNA AND GENETIC INFORMATION
• For organism to survive or live, it must synthesize all the chemicals needed to
operate, maintain, and reproduce cell.
• The cell is like a biological reactor, involving a network of reactions involving
various reactants, products, catalysts and chemical controllers.
• The predominant cell polymers are: lipids, proteins, carbohydrates, nucleic acids
and fats; They are called biological polymers (biopolymers)
NUCLEIC ACIDS
• They are polymers of nucleotides, which are the units that store genetic information in each
cell.
• They contain the hereditary information, hence are also known as informational
biopolymers.
• When the cells divide, a copy of the parent cell’s nucleic acid is passed on the daughter cell.

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• Nucleotides are the building blocks of nucleic acids, and they are also
energy carriers.
• They contain essentially: phosphoric acid, ribose or deoxyribose (5-
carbon sugar), a nitrogenous base.
There are 2 types of nucleic acids
• DNA (deoxyribose nucleic acid), and
• RNA (ribose nucleic acids).
The nucleic acids are macromolecules and polymers of nucleotides
consisting of the 3 components.
The nitrogenous base is derived either from
-Purines (adenine, guanine), or
-Pyrimidines (cytosine, thymine, and uracil)
(Place structures here)
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 85
• RNA is a polymer of ribose containing nucleotides while DNA is a polymer of
deoxyribose containing nucleotides.
• By partial hydrolysis, the nucleotide yields nucleosides containing nitrogen base
attached to a pentose sugar.
• The sugar in DNA is deoxyribose where hydrogen is attached to the second
carbon.
• In the case of RNA, the sugar is ribose in which hydroxyl group (i.e. OH) is bound
to that carbon
• The bases cytosine (C), adenine (A), and guanine (G) are common to both RNA
and DNA. However, RNA molecules contain a unique base, uracil (U), while the
unique DNA base is thymidine or thymine (T).
• These differences in the base structure markedly affect the secondary structure
of these polymers

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Structural differences
• RNA are in the form of a single chain of nucleotides while the DNA
molecules are normally double chain.
• The double chain in DNA allows specific hydrogen bonding between
bases to hold the two strands together. The 2 chains form a double
helix.

(Place structures here)

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 DNA structure
• DNA is a linear polymer of nucleotides linked via phosphodiester bonds.
• The bonds are formed between 3’ and 5’ hydroxyl groups of the ribose moiety
(either of the 2 parts) of the nucleotides.
• DNA is composed of four nucleotides--- adenine (A), thymine (T), guanine (G),
and cytosine (C).
• The primary structure of DNA is the linear sequence of nucleotide residue that
consist of the poly-deoxyribonucleotide chain.
(Place structures here)
• The DNA backbone consists of deoxyribonucleotides linked with covalent
bonding.
• The purines and pyrimidines constitute the side chains.

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• Different sources of DNA molecules differ in terms of the ratio of the four
major types of nucleotide monomers. Hence their molecular weights will also
differ.
• J.D. Watson and FHC Crick postulated the DNA structure with two strands in
complimentary double helical arrangement in 1953.
• DNA varies in length and nucleotide composition, the shortest molecules
being in the order of 103 bases in viruses, 106 in bacteria and 108 in human
beings.
• The polymers are found usually as an aggregated pair of strands that are held
together by hydrogen bonding.
(Place structures here)

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• Watson and crick conceived that DNA molecule has a twisted ladder.
• The upright arms composed of chains of alternating sugars and phosphate
groups.
• The cross bars contain nitrogenous bases, thymine and cytosine as pyrimidine
bases, and adenine and guanine as purine bases.
• The secondary structure of DNA consist of a double-stranded helix formed by
the coiling of two linear poly-deoxyribonucletide strands around an identical
central axis (this form is believed to be predominant form present in living cells).

(Place the double helix structure here)

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• Both strands form right-handed coils, but they are anti-parallel to each other.
• The 5’ end of one strand faces the 3’ end of the other and vice versa.
• DNA is present in procaryotic cells, eucaryotic cells and bacteria in single
chromosome while in eucaryotic cells, it is present in different chromosomes
as different molecules.
• In bacteria, it is generally present in the nucleus.
• The nucleoside “adenosine” has a great biological significance which is made
from ribose and adenine.
• The important derivatives of this nucleoside are adenosine mono-phosphate
(AMP), adenosine diphosphate (ADP), and adenosine triphosphate (ATP).
• The phosphodiester bonds connecting the phosphate groups have useful free
energies of hydrolysis. ATP to ADP has a standard Gibb’s free-energy change of
-7.3 kCal/mol at 37 oC

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• The 2 strands of DNA has opposite polarity.
• Each strand is “template” (pattern) of the other.
• The template form of DNA provides the directions for synthesis of daughter DNA
from a parent DNA molecule, a process called DNA “replication”.
• If 2 complementary DNA strands are separated and double helices are
constructed from them individually, following the base pair rule, the end
products are 2 new molecules.
• Each molecule is identical to original double stranded DNA and each containing
one new strand and one old strand.
• The stands can be separated.
• DNA can also be characterized by heat which separates the double strands. A-T
pairs have 2 hydrogen bonds while G-C base pair have 3.
• A-T rich region melts before G-C regions.
• Melting process could be monitored through absorbance of the DNA solution
at 260 nm.
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 92
• Plasmids are relatively smaller DNAs which are found in many bacteria and
eucaryotes. Bacteria plasmids are circular DNA molecules with very small sizes.
• Plasmids endow their host cells with useful but non-essential functions such as
antibiotic resistance.
• Plasmids are important vehicles of recombinant DNA technology.
• Plasmids can be manipulated in test tubes and if introduced into living cells
genetically, it re-programs the cells and produce new compounds or grow more
efficiently.
• Other small DNA molecules may be inserted into living cells by viruses.
• DNA therefore functions to store instructions for synthesis of RNA molecules of
specific nucleotides sequence and length.
• A sequence of DNA coding for an RNA molecule sequence is called a “gene”.

06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 93

Ribonucleic Acid (RNA)
• Discovered in the year 1955 by Frankel-Conrat and Williams.
• It was assigned a single helical structure, as a result differs from the DNA.
• Unlike DNA, it contains ribose sugars, and the nitrogen group is provided by
Uracil.
• For some viruses like tobacco mosaic, foot-and mouth that contain no DNA,
RNA is the sole genetic molecule that carries the responsibilities of DNA. Such
RNA is known as genetic RNA
For cells in which the genetic substance is DNA, the RNA molecules are called non-
genetic RNA.
There are three types of non-genetic RNAs namely;
-Ribosomal RNA (rRNA)
-Transfer RNA (tRNA), and
-Messenger RNA (mRNA). All the 3 types are synthesized inside the nucleus.
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 94
• RNA does not persist in the cell for very long time (sometimes only for a few
seconds)
• RNA is single stranded and shorter in length.
• The various RNAs which participate in normal cell function serve the purpose
of reading and implementing the genetic instructions of DNA.

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 mRNA
• Complimentary to a basic sequence from a gene in DNA.
• Each mRNA molecule carries a message from DNA to another part of the cell’s
biochemical apparatus.
• Lengths of messages vary, therefore the sizes of mRNA vary ( a chain of say 103 –
104 nucleotides in length is typical).
• The message from mRNA is read in the ribosomes (mostly present on the
endoplasmic reticulum).
• mRNA is a template used by ribosomes for the translation of genetic material
into an amino acid sequence, and it is derived from a specific DNA sequence.
• The genetic code is made up of trinucleotide sequence, or “Codons”, on mRNA.
• Each mRNA has a unique sequence coding for each protein (polypeptide chain).

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rRNA
Up to 65% of the ribosomes is rRNA .
The ribosomal RNA can be separated by a centrifuge into several RNA species.
The role of rRNA is very complex, but is essential for protein synthesis which
occurs within the ribosome organelles.
tRNA
The smallest type of RNA (only 70 to 95 nucleotide components, equivalent to
23,000-30,000 of molecular weight)
Found in cell’s cytoplasm.
Assist in the translation of the genetic code at the ribosomes.

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• tRNA is a single strand of RNA but it is in a folded configuration.
• Each of the 20 amino acids has one or more tRNAs to which it is able to bind.
• In the bound form the amino acids are transported into the ribosomes.
• tRNA molecule therefore serve as adapters for translating the genetic code or
codon of the mRNA into the sequence of amino acids or proteins
• Each tRNA contains a trinucleotide sequence called the “anticodon” sequence,
which is complementary to a codon, the trinucleotide sequence of mRNA that
codes for one amino acid.
• The structures and functions of the various tRNAs and rRNAs in the cells are like
mRNA sequence dictated by the nucleotide sequence of the corresponding
genes in the cell’s DNA.

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• Proteins are the actual biochemical expression of the information and instructions carried by
DNA.
• Compared to the classical process control, proteins are the final control elements which
implement the DNA controller messages to the cellular process.

Biological information storage and DNA replication

• DNA replication is a complex process which requires a number of enzymes and other proteins,
and the participation of RNA.
• It simply means synthesis of daughter DNA from a parent DNA molecule.
• 2 complimentary strands are separated and double helices are constructed from each strand
following the base pairing rules.
• The end products are two new molecules, each identical to the original double stranded DNA,
and each containing one new strand and one old strand.
• The biological message is coded in the DNA nucleotide sequence.
• As the parent strands separate, complimentary strands are added to each parent, resulting in
two daughter molecules identical to the parent.

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• Finally, each daughter molecule contains one strand from the parent.
• The regeneration of DNA from original DNA segments is known as DNA
replication and it is semi-conservative.
• A double stranded DNA molecule looks like the following:
5’ CGAATCGTA 3’
3’ GCTTAGCAT 5’
• Thus, in information sense, knowledge of one strand sequence implies the
sequence of the complimentary strand.
• Each strand is a template for the other.

(Place diagram here)

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• Through molecular genetics, Watson and Crick pointed out that the
flow of information is seen to be essentially in one direction from DNA
to protein.
• Three major steps are defined in the flow of information: replication,
transcription, and translation of the genetic materials.
• Once the replication occurs, the DNA has the information stored in it.
Later on it undergoes a series of changes of transcription and
translation.

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TRANSCRIPTION
• It’s the coping of a complimentary messenger RNA strand on a DNA template
(one of the strands of DNA on which mRNA is transcribed). During transcription
an exact copy is made.
• The process of transcription requires the template, high energy compounds like
ATP, GTP(Guanosinetriphosphate), the enzyme RNA polymerase and divalent
cations.
• RNA polymerase consists of a core enzyme with subunits and sigma factor
• The sigma factor initiates the transcription of mRNA on the DNA template and
the core enzyme continues transcription.
TRANSLATION
• The genetic information in mRNA directs the order of specific amino acids to
form a polypeptide or a protein.
• The process consists of activation of amino acids, transfer of activated amino
acids to tRNA.
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• Initiation of polypeptide chain.
• Chain elongation and termination.
• The processes require ribosomes, mRNA, and tRNA, initiation factors,
termination factors, and high energy compounds like ATP, GTP, and the divalent
ions like Mg2+ .
(Place a sketch of information flow here)

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Differences between RNA and DNA
RNA DNA
1 More primitive than DNA Originated after RNA
2 Is the genetic material of some plants, animals and Is the genetic material of almost all living organisms.
bacterial viruses
3 Except some viruses (e.g. rebovirus) most cellular RNA Except a few viruses, most DNA is double stranded
is single stranded
4 Pentose sugar is ribose Pentose sugar is deoxyribose
5 Bases are A, G, C, U Bases are A, G, C, T
6 Pairing occurs between A-U and G-C Base pairs are A-T and G-C
7 RNA contains a few (12,00) nucleotides Contains millions of nucleotides e.g. over 4 million
8 Base pairing is seen only in hairpin structure and Base pairing occurs throughout the length of DNA
helical region molecule
9 The RNA molecules are of 3 types: rRNA, mRNA, tRNA DNA is only one type
10 The mRNA is found in nucleolus, tRNA and rRNA are DNA is found in chromosomes, mitochondria and
found in cytoplasm. chloroplast

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 RNA DNA
11 RNAs translate the transcripts of DNA into proteins DNA encodes the genetic masses in a form that
transcripts
12 Genetic RNA uses the enzyme reverse transcriptase This enzyme is not required by DNA. DNA after
during replication replication forms DNA and after transcription forms RNA

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 METABOLISM
• Metabolism is a sum of biochemical reactions in living organisms which include
release of energy by breakdown of complex organic compounds into simpler
forms (as Catabolism) and release energy to form new molecules like synthesis
of proteins from amino acids, sugar to polysaccharides (as Anabolism).
• Life support activity of simple organisms involves complex biochemical
reactions.
Catabolism reactions furnish the energy needed to drive anabolic reactions.
• The coupling of energy requiring reactions and electron releasing reactions is
made possible through ATP (Adenosine tri-phosphate)
• ATP stores the energy released by catabolic reactions and makes the energy
available for anabolic reactions and other cellular works.
• ATP is known as the currency of chemical energy in cells.
06/24/2021 CHE323_Introduction to Chemical Engineering 1-Dr. A. O. Ayeni 106
• Bio-energetic deals with energy related processes in organisms.
• Obtaining kinetic energy means all organisms carry out catabolic
processes ( a set of metabolic pathways that break down molecules
into smaller units and release energy)
• Organic substances are broken down into either inorganic substances
or simpler organic compounds having lower level of energy status.
• The liberation of energy from organic substances in a catabolic
process is called RESPIRATION.
• Respiration also provides important intermediates that are required
in the synthesis of several important organic compounds.
• The energy released during respiration is available for the synthesis of
ATP and ADP and inorganic phosphate, and the process is called
oxidative phosphorylation.
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• Respiration can be divided into 2 forms;
aerobic and anaerobic respiration.
• Respiration and fermentation are the two processes taken up by organisms in
producing energy from glucose molecules
• In aerobic respiration the usual mode or mechanism is considered,
• while in anaerobic respiration, also termed fermentation it is obligatory in a few
organisms.
• During anaerobic respiration, the substrate which is usually glucose is
completely oxidized to form the intermediates, later producing ethanol and
carbon dioxide.
• Glycolysis is the process of breakdown of glucose for the production of pyruvic
acid using the pathways
• Glycolysis is also called Embden-Meyerhof-Parnas (EMP) pathway
• The most common glycolysis pathway is EMP. There are others.
• Krebs cycle are some of the processes which are part of bioenergetics
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 Glycolytic process
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 Glycolytic process

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 Glycolytic process

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 • EMP Pathway consists of two steps:
Step 1: Conversion of carbohydrate or glucose to fructose-1, 6- diphosphate, and
also biphosphate
Step 2: Conversion of fructose-1,6-diphosphate into 2 molecules of pyruvic acid
• When glucose is converted to pyruvic acid, free energy is released
• The free energy is used to form the high-energy molecules adenosine
triphosphate (ATP) and reduced nicotinamide adenosine dinucleotide (NAD)
• Glycolysis is a sequence of ten reactions catalyzed by enzymes.
• Both respiration and fermentation starts with the glycolytic pathway wherein
glucose is broken down to pyruvic acid in series of steps.
• Fermentation is an anaerobic oxidation of pyruvic acid to produce lactic acid
(lactic acid fermentation process)

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 Lactic acid Fermentation (Pyruvic acid to lactic acid)
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 Significance of glycolysis (EMP pathway)
1. Glycolysis forms the prelude to both aerobic and anaerobic kinds of
respiration
2. From one molecule of glucose, two molecules of pyruvic acid and two
molecules of ATP are formed
3. A total of 8 ATP molecules are yielded during the process of glycolysis

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 Aerobic oxidation of pyruvic acid (Krebs cycle)
• In the presence of molecular oxygen, the pyruvic acid which is produced in
glycolysis is completely oxidized to carbon dioxide and water
• Krebs (1940), gave a scheme for oxidation of pyruvic acid by means of a cycle of
organic acids.
• This cycle is known as the tricarboxylic acid cycle (TCA) and citric acid cycle (CAC)
• TCA or the Krebs cycle takes place inside the mitochondria where all the
necessary enzymes are present

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 Kreb cycle

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 Kreb cycle

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 Kreb cycle

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Hexose monophosphate (HMP) pathway
• The pentose phosphate pathway (also called the phosphogluconate
pathway and the hexose monophosphate (HMP) shunt) is a metabolic pathway
 parallel to glycolysis
• It is an alternative pathway of oxidation of glucose taking place in the cytoplasm
of the cell
• It generates NADPH and pentoses (5-carbon sugars) as well as 
ribose 5-phosphate, a precursor for the synthesis of nucleotides
• While the pentose phosphate pathway does involve oxidation of glucose, its
primary role is anabolic rather than catabolic. 
• The pathway is especially important in red blood cells (erythrocytes).

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