Overview of biological basics (for engineers)

1. 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)

2. 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?

3. Primary Cell Types:

4. 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)

5. Primary Cell Types: Cyanobacteria (blue-green algae)

6. 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

7. Eucaryotes:

8. Eucaryotes:

9. 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)

10. 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: P. rogueforti ATCC 6987, P. rogueforti ATCC 9295, P. rogueforti ATCC 10110 and P. rogueforti NRRL 849

11. 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)

12. Cell Construction Living cell structural elements include the following macromolecules: - polysaccharides - lipids - proteins - nucleic acids - storage materials including fats, polyhydroxybutyrate, and glycogen.

13. Cell Construction See page 6 of the handout titled “Organic chemistry, Biochemistry”

14. 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.

15. Cell Construction: carbohydrates

16. 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.

17. 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.

18. 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.

19. 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. Cellulose

20. Amino group Carboxyl group H H O H N C C OH R -carbon Side chain 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 Structure of amino acid:

21. R2 H H O H N C C OH H N C C OH H H O R1 R2 H H O- H N C C N C C OH R1 H+ H O 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. + + H2O Peptide bond

22. 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.

23. 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.

24. Cell Construction: lipids

25. 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.

26. 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)

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

28. 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

29. 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

30. 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

31. 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

32. Macronutrients: nitrogen Most common nitrogen sources in industrial fermentation: - yeast extract - soya meal - fish solubles and meal - groundnut meal

33. 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

34. 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

35. 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 10-4M)

36. 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

37. 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

38. 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

39. 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

40. 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 protozoa