Transcript ppt_Set_06 - rshanthini

CP504 – ppt_Set 06
Overview of
biological basics (for engineers)
Learn the following about microorganisms:
- primary cell types
- microbial diversity
- materials of cell construction (carbohydrates,
proteins, lipids, nucleic acids)
- cell nutrients (carbon, nitogen, oxygen, hydrogen
and other)
- micorbes (bacteria, actinomycetes, fungi, algae,
protozoa, rotifers and viruses)
Prof. R. Shanthini
30 Nov 2012
We saw earlier in this lecture series:
“One of the dishes was contaminated by a common
mold of the Penicillium genus” which lead to the
discovery of penicillin
What is a mold?
What is Penicillium genus?
Or, better ask what is meant by Micro-organisms (microbes nickname) or Cells?
Prof. R. Shanthini
30 Nov 2012
Primary Cell Types:
Prof. R. Shanthini
30 Nov 2012
Primary Cell Types:
Procaryotes:
- mostly bacteria
- single celled
- 0.5 – 3 micrometers in equivalent radius
- No membrane around the genetic material (DNA)
- grow rapidly (doubling time: ½ hour to several hours)
- carbon source include carbohydrates, hydrocarbons,
proteins and CO2
Eg:
Eschericia coli (E. coli);
Cyanobacteria (blue-green algae)
Prof. R. Shanthini
30 Nov 2012
Primary Cell Types:
Cyanobacteria (blue-green algae)
Prof. R. Shanthini
30 Nov 2012
Primary Cell Types:
Eucaryotes:
- fungi (yeasts and molds), algae and protozoa are
single-celled eucaryotes
- animal and plant cells are multi-cellular eucaryotes
- 5 to 10 times larger than procaryotes
Prof. R. Shanthini
30 Nov 2012
Eucaryotes:
No cell walls
No chloroplasts
No chlorophyll
Most of cell is cytoplasm
Prof. R. Shanthini
Small
(if any) vacuoles
30 Nov 2012
Rigid cell walls
Green chloroplasts
Contains chlorophyll
Thin lining of cytoplasm
Vacuole filled with cell sap
Eucaryotes:
Prof. R. Shanthini
30 Nov 2012
Microbial Diversity
- Aerobic microbes (love oxygen, and die without oxygen)
- Anaerobic microbes (oxygen is toxic)
- Facultative microbes (can live with and without oxygen)
- Psychrophiles (love cold, grow best at cold temperatures)
- Mesophiles (grow best in moderate temperatures)
- Thermophiles (love heat, grow best at high temperatures)
- Extremophiles (loves extreme conditions)
- coccus, cocci (spherical/elliptical)
- bacillus, bacilli (cylindrical/rod)
- spirillum, spirilla (spiral)
Prof. R. Shanthini
30 Nov 2012
Genus/Species/Strains
Species – organisms that are substantially alike
Eg: Penicillium notatum (P. notatum)
Penicillium chrysogenum (P. chrysogenum)
Penicillium roqueforti (P. rogueforti)
Genus – group of related species
Eg: Penicillium genus
Strains/Substrain – variation within species
Eg:
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30 Nov 2012
P. rogueforti ATCC 6987,
P. rogueforti ATCC 9295,
P. rogueforti ATCC 10110 and
P. rogueforti NRRL 849
Viruses
- very small (30 to 200 nm)
- parasitic
- lie in the boarder of living organisms and chemical compounds
- need host cell to be functionally active and not free-living
- DNA or RNA covered by a protein coat
- DNA gets incorporated into the host DNA
- agents of deceases
- difficult to remove because they are so small and so resistant
to normal disinfection
- wastes that may contain viruses are sewage, hospital wastes
and effluents from food-processing facilities.
- and more…. (could be an assignment topic)
Prof. R. Shanthini
30 Nov 2012
Cell Construction
Living cell structural elements include the following
macromolecules:
- polysaccharides
- lipids
- proteins
- nucleic acids
- storage materials including fats, polyhydroxybutyrate,
and glycogen.
Prof. R. Shanthini
30 Nov 2012
Cell Construction
Example of a
Macromolecule
Monomer
polysaccharide
(complex carbohydrate)
monosaccharide
(simple sugar)
fat (a lipid)
glycerol, fatty acid
protein
amino acid
nucleic acid
nucleotide
Prof. R. Shanthini
30 Nov 2012
See page 6 of the handout titled
“Organic chemistry, Biochemistry”
Cell Construction: carbohydrates
- general formula is (CH2O)n
- Monosaccharides are simple sugars, having 3 to 9 carbon
atoms.
- Examples are glucose, fructose and galactose with the
structural formula is C6H12O6.
Prof. R. Shanthini
30 Nov 2012
Cell Construction: carbohydrates
Prof. R. Shanthini
30 Nov 2012
Cell Construction: carbohydrates
Energy from glucose is obtained from the oxidation reaction
C6H12O6 + 6O2 --> 6CO2 + 6H2O;
ΔG = 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.
Prof. R. Shanthini
30 Nov 2012
Cell Construction: carbohydrates
- Disaccharides are composed of 2 monosaccharides joined
together by a condensation reaction.
- Example: Sucrose (table sugar) is composed of glucose and
fructose.
Prof. R. Shanthini
30 Nov 2012
Cell Construction: carbohydrates
- Polysaccharides are long chain macromolecules formed by
the bonding of many, many monosaccharides by successive
condensation reactions.
- 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.
- Plants produce starch to store carbohydrates.
Prof. R. Shanthini
30 Nov 2012
Cell Construction: carbohydrates
-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.
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Cellulose
Cell Construction: proteins
- Protein molecules consist of one or more polypeptides put
together typically in a biologically functional way (and
sometimes have non-peptide groups attached)
- A polypeptide is a single linear chain of amino acids
bonded together by peptide bonds
Amino
group
Carboxyl
group
H H O
Structure of amino acid:
H N C C OH
R
Prof. R. Shanthini
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Side
chain
-carbon
A peptide bond is a covalent chemical bond formed between two
molecules when the carboxyl group [-C(=O)OH] of one molecule
reacts with the amino group [-NH2] of the other molecule,
causing the release of a molecule of water (H2O), and usually
occurs between amino acids.
R2
H H O
H
N
C
C
OH + H
R1
H
H
H
O-
N
C
C
R1
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N
C
C
H
H
O
OH
R2
N
C
C
H+ H
O
OH
+
Peptide bond
H2O
Cell Construction: lipids
- Lipids are compounds that are insoluble in water but soluble
in nonpolar solvents.
- Some lipids function in long-term energy storage. One gram
of fat stores more than twice as much energy as one gram of
carbohydrate.
- Lipids are also an important component of cell membranes.
Prof. R. Shanthini
30 Nov 2012
Cell Construction: lipids
- Fats and oils are composed of fatty acids and glycerol
- Fatty acids have a long hydrocarbon (carbon and
hydrogen) chain with a carboxyl (acid) group. The chains
usually contain 16 to 18 carbons.
- Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts
with 3 fatty acids to form a triglyceride or fat molecule.
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Cell Construction: lipids
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Cell Construction: nucleic acids
DNA (deoxyribonucleic acid) is the genetic material.
An important function of DNA is top store information
regarding the sequence of amino acids in each of the body’s
proteins.
This "list" of amino acid sequences is needed when proteins
are synthesized.
Before protein can be synthesized, the instructions in DNA
must first be copied to another type of nucleic acid called
messenger RNA.
Prof. R. Shanthini
30 Nov 2012
Cell Nutrients
- 80% of cell material is water
- Macronutrients are C,N,O,H,S,P, Mg, K
(required at > 10-4M)
- Micronutrients are Mo, Zn, Cu, Mn, Ca, Na,vitamins, growth
hormones, metabolic precursors
(required at < 10-4M)
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30 Nov 2012
Macronutrients: carbon
- major cellular material
- major source of energy
- derived primarily from carbohydrates, lipids, hydrocarbons
and CO2
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30 Nov 2012
Macronutrients: carbon
Heterotrophs:
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 conditions
Prof. R. Shanthini
30 Nov 2012
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
Prof. R. Shanthini
30 Nov 2012
Macronutrients: carbon
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
Prof. R. Shanthini
30 Nov 2012
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 in incorporated into cell mass in the form of proteins
(inclusive of enzymes) and nucleic acids
- some microbes (eg. Cyanobacteria) fix nitrogen from the
atmosphere to form ammonium
- urea is also used as a nitrogen source by some organisms
- organic nitrogen sources (yeast extract and peptone) are
expensive compared to ammonium salts
Prof. R. Shanthini
30 Nov 2012
Macronutrients: nitrogen
Most common nitrogen sources in industrial fermentation:
- yeast extract
- soya meal
- fish solubles and meal
- groundnut meal
Prof. R. Shanthini
30 Nov 2012
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 sparging
air or by surface aeration
Prof. R. Shanthini
30 Nov 2012
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
Prof. R. Shanthini
30 Nov 2012
Micronutrients (or trace elements):
- lack of essential micronutrients increases the lag phase,
decreases the specific growth arte 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)
Prof. R. Shanthini
30 Nov 2012
Microbes: bacteria
- bacteria are the smallest living organisms
- found in excess of 106 bacteria per ml of wastewater
- bacteria provide the largest component of the microbial
community in all biological wastewater treatment processes
- hydrogen from waste can be produced using a
bacterium called Caldicellulosiruptor saccharolyticus
Prof. R. Shanthini
30 Nov 2012
Microbes: actinomycetes
- actinomycetes are filamentous bacteria
- they play an important role in degrading complex organics
such as cellulose, lignin, chitin, and proteins
- their enzymes enable them to chemically break down tough
debris such as woody stems, bark, or newspaper, and therefore
important in composting
Prof. R. Shanthini
30 Nov 2012
Microbes: fungi
- fungi are important because they break down tough debris,
enabling bacteria to continue the decomposition process
- yeast is used in the production of bread and liquor
- penicillium species are used for giving flavor, aroma and
characteristic color to some cheese
- some fungi are source of antibiotics and some other drugs
(Penicillin, Lovastatin, Cyclosporine, Ergotine and Griseofulvin)
- yeats are heavily used in genetic and molecular biological
research
Prof. R. Shanthini
30 Nov 2012
Microbes: algae
- algae are plants which use sunlight for the photosynthesis of
new organic material from carbon dioxide, nitrogen compounds
and phosphates
- they produce oxygen and so react synergistically with
bacteria, fungi and animals which consume oxygen and
produce carbon dioxide and nitrogen compounds.
- algae have colours, blue-green, green, yellow-green, and
require phosphorus for growth
- they store far more phosphorus than they need for growth and
this is returned to the water when the algae die, leading to
eutrophication
Prof. R. Shanthini
30 Nov 2012
Microbes: protozoa and rotifers
- protozoa are one-celled microscopic animals
- they obtain their food from organic matter in the same way as
bacteria do, but also act as secondary consumers ingesting
bacteria and fungi
- protozoa, in many wastewater treatment processes, act as
polishing agents by grazing on free-swimming bacteria
- the simplest multi-cellular animals are rotifers
- they feed on organic matter and also digest bacteria and fungi
rotifer
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30 Nov 2012
protozoa