Overview of

biological basics (for engineers)

Learn the following about microorganisms:
1. primary cell types
Microbiology
2. microbial diversity
3. micorbes (bacteria, actinomycetes, fungi,
algae, protozoa, rotifers and viruses)
Biochemistry 4. materials of cell construction
and Organic
Chemistry (water, carbohydrates, lipids,
proteins, nucleic acids)
5. cell nutrients (carbon, nitogen, oxygen,
hydrogen and other)
1
Materials of cell construction

Mainly:
Water

Carbon based molecules

2
 Water
About 60-90 percent
of an organism is
water
Water is used in
most reactions in
the body
Water is called
the universal
solvent
3
Carbon-based Molecules
Although a cell is
mostly water, the rest
of the cell consists
mostly of carbon-
based molecules

Organic chemistry
is the study of
carbon compounds
4
Carbon is a Versatile Atom
It has four electrons in
an outer shell that holds
eight electrons

Carbon can
share its
electrons with
other atoms to
form up to four
covalent bonds
5
Carbon can use its bonds to:

Attach to other
carbons

Form an
endless
diversity of
carbon
skeletons

6
Shape of Organic Molecules
Each type of organic
molecule has a
unique three-
dimensional shape

The shape
determines its
function in an
organism

7
Common Functional Groups

8
 Giant Molecules - Polymers
Large molecules are
called polymers
Polymers are built
from smaller
molecules called
monomers

Biologists call
them
macromolecules
9
 Macromolecules in Organisms
There are 4 categories in cells:

1. Carbohydrates (mono-, di- and poly-

saccharides)
2. Lipids (fats, waxes, steroids & oils)

3. Proteins (hormons, enzymes)

4. Nucleic Acids (DNA, RNA)

10
Macromolecules in Organisms

Macromolecule Monomer
Carbohydrate Monosaccharide
(simple sugar)

Lipid Glycerol and Fatty acid

Protein Amino acid

Nucleic acid Nucleotide

11
1. Carbohydrates

12
 1. Carbohydrates
Monosaccharides:
Called simple sugars
Include glucose,
fructose, & galactose

Have the same

chemical, but
different structural
formulas called an
isomer.
C6H12O6
-general formula is (CH2O)n 13
 Monosaccharides
Glucose is found in
sports drinks
Fructose is found
in fruits
Honey contains
both glucose &
fructose
Galactose is called
milk sugar
14
 Carbohydrates
Carbohydrates include:
Small sugar molecules
in soft drinks
Long starch molecules in
pasta and potatoes

15
 Rings
In aqueous (watery) solutions,
monosaccharides form ring structures

16
Rings

17
 Cellular Fuel

Monosaccharides
are the main fuel
that cells use for
cellular work

ATP
18
 Cellular Fuel
Energy from glucose is obtained from the oxidation reaction

C6H12O6 + 6O2 --> 6CO2 + 6H2O; G = 2870 kJ.

In living organisms, the oxidation of glucose contributes to a

series of complex biochemical reactions.

These reactions provide the energy needed by cells.

19
 Disaccharides
A disaccharide is a
double sugar

Theyre made by
joining two
monosaccharides

Involves removing
a water molecule
(dehydration)
20
 Disaccharides

Common disaccharides include:

Sucrose (Table sugar)

Lactose (Milk Sugar)
Maltose (Grain sugar)
21
 Polysaccharides
Complex
carbohydrates
Composed of many
sugar monomers
linked together
Polymers of
monosaccharide
chains

22
Examples of Polysaccharides
Glucose Monomer

Starch

Glycogen

Cellulose

23
 Examples of Polysaccharides

- Starch and glycogen are polysaccharides that function to

store energy. They are composed of alpha-glucose
monomers bonded together producing long chains.
- Animals store extra carbohydrates as glycogen in the
liver and muscles. Between meals, the liver breaks down
glycogen to glucose in order to keep the concentration of
glucoses in the blood stable.

24
 Examples of Polysaccharides
-Cellulose and Chitin are polysaccharides that function to
support and protect the organism.
- The cell walls of plants are composed of cellulose. The cell
walls of fungi and the exoskeleton of arthropods are
composed of chitin.
- Cellulose is composed of beta-glucose monomers in such a
way that the molecule is straight and unbranched.

25
Cellulose
 Sugars in Water
Simple sugars and double sugars dissolve
readily in water WATER
MOLECULE

They are
hydrophilic,
or water-
loving

SUGAR
MOLECULE

26
 Intake Excess Sugars
Diabetes occurs when the pancreas does not produce
enough of the hormone insulin, or the body cant use insulin
properly.

Insulin helps carry sugar from the bloodstream into the

cells. Once inside the cells, sugar is converted into energy
for immediate use or stored for the future. That energy fuels
many of our bodily functions.

For excess blood sugar, the pancreas is overdrive, which

can result in total-body inflammation that, in turn, puts the
pancreas cells inactive.

https://youtu.be/mNYlIcXynwE
27
 Intake Excess Sugars

It overloads and damages your liver

It tricks your body into gaining weight and affects your

insulin signaling.

It causes metabolic dysfunction: high blood pressure.

It increases your uric acid levels: High uric acid levels are a
risk factor for heart and kidney disease.

28
2. Lipids

29
 2. Lipids
Lipids are hydrophobic water fearing
Do NOT mix with water

Includes fats,
waxes,
steroids, &
oils

Soluble in nonpolar solvents.

FAT MOLECULE
30
 Function of Lipids
Fats store energy, help to insulate the
body, and cushion and protect organs

Lipids are also an important component of cell

membranes
31
 Lipids & Cell Membranes
Cell membranes are made of
lipids called phospholipids
Phospholipids have a head
that is polar & attract water
(hydrophilic)
Phospholipids also have 2
tails that are nonpolar and do
not attract water
(hydrophobic)

Copyright Cmassengale 32
Cell membrane with proteins &
phospholipids

33
 Monomer of Lipids

Composed of:
Glycerol
3 fatty acid chains

34
 Fatty Acids
Fatty acids have a long hydrocarbon (carbon and
hydrogen) chain with a carboxyl (acid) group. The
chains usually contain 16 to 18 carbons.
Unsaturated fatty acids have less than the
maximum number of hydrogens bonded to
the carbons (a double bond between
carbons)
Saturated fatty acids have the
maximum number of hydrogens
bonded to the carbons (all single
bonds between carbons) 35
Types of Fatty Acids

Single
Bonds in
Carbon
chain

Double bond in carbon

chain
36
 Glycerol

Glycerol forms the

backbone of the
fat
-Glycerol contains 3
carbons and 3 hydroxyl
groups. It reacts with 3
fatty acids to form a Organic Alcohol
triglyceride or fat
molecule.
37
Triglyceride

38
 Triglyceride

Glycerol Fatty Acid Chains

39
 Fats in Organisms
Most animal fats have a high proportion of
saturated fatty acids & exist as solids at
room temperature (butter, margarine,
shortening)

40
 Fats in Organisms
Most plant oils tend to be low in saturated
fatty acids & exist as liquids at room
temperature (oils)

41
 Steroids
The carbon skeleton
of steroids is bent to
form 4 fused rings
Cholesterol

Cholesterol is
the base Estrogen
steroid from Testosterone

which your body

produces other
steroids
Estrogen & testosterone are also steroids
42
 Synthetic Anabolic Steroids
They are variants of
testosterone
Some athletes use
them to build up
their muscles quickly

They can pose

serious health risks

43
3. Proteins

44
 3. Proteins
Proteins are polymers made of monomers
called amino acids

All proteins are made of 21 different

amino acids linked in different orders
Proteins are used to build cells, act
as hormones & enzymes, and do much
of the work in a cell
Proteins carry out most
activities of life 45
21 Amino Acid Monomers

46
21 Amino Acid Monomers

47
 Four Types of Proteins
Storage

Structural

Contractile
Transport
48
 Structure of Amino Acids
Amino Carboxyl
Amino acids have a group group
central carbon with 4
things boded to it: R group

Amino group NH2

Carboxyl group -COOH

Hydrogen -H Side
groups
Side group -R Serine-hydrophillic
Leucine -hydrophobic
49
 Linking Amino Acids
Carboxyl
Cells link amino
acids together to Amino
make proteins Side
Group
The process is
called condensation Dehydration
or dehydration Synthesis

Peptide bonds
form to hold the
amino acids
together
Peptide Bond 50
 Proteins as Enzymes
Many proteins act as biological catalysts
or enzymes
Thousands of different enzymes exist
in the body
Enzymes control the rate of chemical
reactions by weakening bonds, thus
lowering the amount of activation
energy needed for the reaction

51
 Enzymes
Enzymes are globular proteins.

Their folded conformation creates an

area known as the active site.

The nature and arrangement of amino

acids in the active site make it specific
for only one type of substrate.

52
Enzyme + Substrate = Product

53
Protein Structures or CONFORMATIONS

Hydrogen bond

Pleated sheet
Polypeptide
Amino acid (single subunit)

(a) Primary structure

Hydrogen bond

Alpha helix

(b) Secondary (c) Tertiary

structure structure

(d) Quaternary structure

54
 Denaturating Proteins
Changes in temperature & pH can
denature (unfold) a protein so it no
longer works
Cooking denatures
protein in eggs

Milk protein separates into

curds & whey when it
denatures
55
 Other Important Proteins
Blood sugar level is controlled by a
protein called insulin
Insulin causes the liver to uptake and
store excess sugar as Glycogen
The cell membrane also contains
proteins
Receptor proteins help cells
recognize other cells
Antibodies are proteins that bind to
particular molecules 56
4. Nucleic Acids

57
 4. Nucleic Acids
Store hereditary information
Contain information for making
all the bodys proteins

Two types exist ---

DNA & RNA

DNA: deoxyribonucleic acid

RNA: ribonucleic acid 58
 DNA
DNA is often called the
blueprint of life
Components of genes
Polymers of nucleotides
Director of protein synthesis

Proteins carry out most

activities of life

59
 DNA
Two strands of DNA join
together to form a
double helix or ladder
Base
pair

Double helix

Ladder
60
 Why do we study DNA?
We study DNA for
many reasons,
e.g.,
its central
importance to all
life on Earth
medical benefits
such as cures for
diseases
better food crops.
61
 DNA
Nitrogenous base
(A,G,C, or T)

DNA: polymers
of nucleotides Thymine (T)
Phosphate
group

Sugar
(deoxyribose)
Phosphate

Base
Sugar

Nucleotide 62
Nucleotide Nucleic acid monomer

63
 Bases
Each DNA
nucleotide has one
of the following
bases:
Thymine (T) Cytosine (C)
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
Adenine (A) Guanine (G)
64
 Nucleotide Monomers
Backbone

Form long chains Nucleotide

called DNA

Nucleotides are
joined by sugars
& phosphates on
the side
Bases

DNA strand 65
 DNA Double Helix
5 O 3

H-bonds
3 O
P 5 P
5 O
1 G C 3
2
4 4
2 1
3 5
O
P P
5
T A 3

O
5
P 3 P
 DNA Double Helix
The phosphate and sugar
form the backbone of the DNA Rungs of ladder
molecule, whereas the bases
form the rungs. Nitrogenous
Base (A,T,G or C)

Legs of ladder

Phosphate &
Sugar Backbone
BASE-PAIRINGS
H-bonds

G C

T A
 BASE-PAIRINGS
A---? A---T
G---? G---C
C---? C---G
T---? T---A
A---? A---T
G---? G---C
A---? A---T
G---? G---C
C---? C---G
A---? A---T
G---? G---C
T---? T---A 69
RNA

70
 RNA Ribonucleic Acid
Nitrogenous base
(A,G,C, or U)
Ribose sugar
has an extra
OH or
hydroxyl
group
Uraci
It has the
Phosphate
group l
base uracil (U)
instead of
thymine (T) Sugar (ribose)

71
 DNA vs RNA
Difference between DNA and RNA.
DNA Double Helix, RNA Single Stranded
DNA --- A-T, RNA ---A-U
DNA ---Deoxyribose Sugar, RNA---Ribose

What is a similarity of DNA and RNA?

G binds with C in both DNA and RNA
Both have sugar and phosphate backbone
Structure of RNA

73
 Three Types of RNA
.

Messenger RNA (mRNA) copies DNAs

code & carries the genetic information to
the ribosomes
Ribosomal RNA (rRNA), along with
protein, makes up the ribosomes (major
component of ribosome)
Transfer RNA (tRNA) transfers amino
acids to the ribosomes where proteins
are synthesized

74
 Ribosome- site of protein synthesis

75
 Chromosomes, Genes and
See p. 297
Chromosomes
Proteins
Chromosomes are tightly
bound, coiled DNA

Human beings have 23 pairs

of chromosomes in every
cell, which makes 46
chromosomes in total

The sex chromosomes

determine whether you are a boy (XY)
or a girl (XX)
 Chromosomes, Genes and
Proteins
Genes
Genes are long strands of DNA on
chromosomes
The species-particular DNA sequences
produce the species-particular proteins
Genes code for proteins
 Chromosomes, Genes and
Proteins
Codon
The bases on the m-RNA are arranged in triplets called
codons (which code for a specific AMINO ACID)

AGG-CTC-AAG-TCC-TAG
TCC-GAG-TTC-AGG-ATC

A codon designates an amino acid

An amino acid may have more than one codon

AMINO ACIDS are the building blocks of proteins.

78
 The Genetic Code

Use the code by

reading from the
center to the outside

Example: AUG codes

for Methionine

79
How Protein synthesis?

Transcription
and
Translation

81
Pathway to Making a Protein
Transcription Translation

Short lived
83
 AMAZING DNA FACTS

Each cell has about 2 m

of DNA.

The average human has

75 trillion cells.

The average human has

enough DNA to go from The earth is 150 billion m
the earth to the sun or 93 million miles from
more than 400 times. the sun.

84
 AMAZING DNA FACTS
It contains information
equal to some 600,000
printed pages of 500 words
each!!!
(a library of about 1,000 books)
Summery of Macromolecules

86
Summery of Macromolecules

87
88
Overview of
biological basics (for engineers)
Learn the following about microorganisms:
1. primary cell types
2. microbial diversity
Microbiology
3. micorbes (bacteria, actinomycetes, fungi,
algae, protozoa, rotifers and viruses)
4. materials of cell construction (carbohydrates,
lipids, proteins, nucleic acids)
Biochemistry 5. cell nutrients (carbon, nitogen,
oxygen, hydrogen and other)
89
5. Cell Nutrients
- all organisms (except virus): 80% of cell material is water

- Macronutrients are C,N,O,H,S,P, Mg+2, K+

(required at > 10-4M)

- Micronutrients are Mo+2, Zn+2, Cu+2, Mn+2, Ca+2,

Na+,vitamins, growth hormones, metabolic precursors
(required at < 10-4M)

90
 Macronutrients: carbon
- major cellular material
- major source of energy
- derived primarily from carbohydrates, lipids, hydrocarbons
and CO2

91
 Macronutrients: carbon
Microorganisms are classified on the basis of carbon source:
Heterotrophs:
These organisms use carbohydrates, lipids and
hydrocarbons as a carbon and energy source

Autotrophs:
Chemoautotrophs: use CO2 as a carbon source and obtain
energy from the oxidation of inorganic compounds
Photoautotrophs: use CO2 as a carbon source and utilize
light as an energy source
Mixotrophs:
grow under both autotrophic and heterotrophic
92
conditions
 Macronutrients: carbon

Most common carbon sources in industrial fermentation:

- molasses (sucrose)
- starch waste (glucose and dextrin)
- whey
- cellulose waste

Most common carbon sources in laboratory fermentation:

- glucose
- sucrose
- fructose
93
In aerobic fermentation:
- 50% of substrate carbon is converted to cell mass
- 50% of substrate carbon is used as an energy source

In anaerobic fermentation:
- a large fraction of substrate carbon is converted to products
- a smaller fraction (< 30%) is converted to cell mass

94
 Macronutrients: nitrogen
nitrogen is about 10 to 14% of cell dry weight.
most widely use nitrogen sources are ammonia, or the
ammonium salts (NH4Cl, (NH4)2SO4, NH4NO3), proteins,
peptides, and amino acids.
nitrogen is incorporated into cell mass in the form of
proteins (inclusive of enzymes) and nucleic acids.
some microbes (eg. cyanobacteria, azotobacter sp.) fix
nitrogen from the atmosphere to form ammonium.
urea is also used as a nitrogen source by some
organisms
organic nitrogen sources (e.g.,yeast extract and peptone)
are expensive compared to ammonium salts
95
 Macronutrients: nitrogen

Most common nitrogen sources in industrial fermentation:

- yeast extract
- soya meal
- fish solubles and meal
- groundnut meal
- cottonseed extract

96
 Macronutrients: oxygen
- oxygen is about 20% of cell dry weight
- oxygen is required for the water (almost 80%) in the cell
- molecular oxygen is required in aerobic reactions
- gaseous oxygen in introduced into growth media by sparing
air or by surface aeration

Macronutrients: hydrogen
- hydrogen is about 8% of cell dry weight
- hydrogen is required for the water (almost 80%) in the cell
- derived primarily from carbon sources (eg. carbohydrates
- some bacteria (eg. methanogens) utilizes hydrogen as an
energy source 97
 Other Macronutrients:
Phosphorus (P)
- P is about 3% of cell dry weight
- present in nucleic acid and in the cell wall
- key element in the regulation of cell metabolism
- common source: KH2PO4, K2HPO4

Sulfur (S)
- about 1% of cell dry weight
- present in proteins and in some coenzymes
- certain autotrophs utilize S as energy source
- common source: (NH4)2SO4
Enzyme helper:
Cofactor: inorganic source (e.g., metal ions)
Coenzymes : organic source (e.g., vitamins) 98
 Other Macronutrients:
Potassium (K)
- K is cofactor for some enzymes
- required for carbohydrate metabolism
- common source: KH2PO4, K2HPO4 and K3PO4

Magnesium (Mg)
- cofactor for some enzymes
- present in cell walls and membranes
- ribosomes specifically require Mg+2
- common source: MgSO4. 7H2O, MgCl2

99
100
Micronutrients (or trace elements):
- lack of essential micronutrients increases the lag phase,
decreases the specific growth rate and yield
- most widely needed are Fe, Zn and Mn.
- needed under specific growth conditions are Cu, Co, Mo, Ca,
Na, Cl, Ni and Se
- rarely required are B, Al, Si, Cr, V, Sn, Be, F, Ti, Ga, Ge, Br,
Zr, W, Li and I (toxic at greater than 10-4 M)

101
 Growth Media

Oxygen Carbon dioxide

Carbon and
Energy Biomass
Sources

Nitrogen
Source CELL Metabolite(s)

Water
Other
requirements
(P, Heat
S,Na,K,Mg,etc
)
102
 Mammalian Cells Cultivation

Cells as an end product Cells-derived product

Ex. Stem cells
Artificial skin Growth factors
Artificial organ Hormones
-Hepatocyte (liver) -Human growth hormones
-Beta-islet cells (pancreas) -Insulin
Bone Marrow Interferons
Lymphocytes Monoclonal antibodies

103
Different levels for mammalian cells
cultivation
Small scale (T-flask, 2

24 well plate

T-flask Scaling up
104
Plant Cells Cultivation
PhotoBioreactor
- Plant cells

- Algal cells

1
0
 Different levels of cells cultivation
Cell Productivity

Non-Optimized
Small scale (T-flask, 24 well)
Shear Stress

Spinner flask Rolling bottles Semi-Optimized

Mixing

Bioreactor Level Fully-Optimized

(STR, Air-Lift, Hollow fiber)

106
107