BIOCHEM CH2 OVERVIEW OF MICROBIOLOGY.pdf
- 1. 1 Analysis of Biological System Part I: Overview of Microbiology Chapter 2 Introduction,, Naming, Microbial diversity, Procaryotes, Eucaryotes, Reproduction
- 2. 2Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Analysis of Biological System An understanding of biological system can be simplified by analyzing the system at several different levels: „ Cell level: microbiology, cell biology; „ Molecular level: biochemistry, molecular biology; „ Population level: microbiology, ecology; „ Production level: bioprocess.
- 3. 3Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Course Outline „ Overview of Microbiology „ Biochemistry of Cells „ Enzyme Technology „ Molecular Biology and Metabolic Pathways „ Microbial Growth Models „ Bioreactor Analysis and Operation „ Downstream Processing (product recovery and purification) „ Genetic Engineering
- 4. 4Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Overview of Microbiology „ Microbiology (in Greek micron = small and biologia = studying life) is the study of microorganisms at the cell level. „ Microorganism refers to any organism too small to be viewed by the unaided eye, as bacteria, fungi and algae and protozoa. It is often illustrated using single-celled, or unicellular organisms
- 5. 5Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Cell: „ The cell is the basic unit of life. „ Cells are packages of living matter surrounded by membranes or walls. „ Within the cell are various organelles in controlling life processes for the cell intake of nutrients, production of energy, discharge of waste materials, and reproduction.
- 6. 6Chapter 2 Part I Basics of Microbiology „ Naming cells „ Primary classification of microorganism - Procaryotes: bacteria; - Eucaryotes: fungi (yeast and mold) algae - Virus „ Microbial cell characteristics under each cell category - cell structure and reproduction JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 7. 8Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Microbial diversity Cell adaptation to the environment Temperature „ Psychrophiles can grow below 20oC. e.g. Leifsonia rubra isolated from Antarctica. „ Mesophiles grow between 20-50oC. important uses in food preparation such as cheese, yoghurt, beer and wine making, e.g. Saccharomyces cerevisiae. „ Thermophiles can grow at temperature higher than 50oC. Thermus aquaticus is a species of bacterium that can tolerate high temperatures. It thrives at 70°C, but can survive at temperatures 50°-80°C . Regular sterilization at 121oC.
- 8. 9Chapter 2 Part I pH: ‰ Acidophiles are microbes that tends toward acidic conditions pH < 3. e.g Acidithiobacillus ferrooxidans in acid mine drainage. ‰ Alkaliphiles are microbes that thrive in alkaline environments with a pH of 9 to 11. e.g. Bacillus okhensis living in carbonate soil. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Moisture: Some cells can grow - where the water activity is high (e.g. algae) - on solid surface (mold)
- 9. 10Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Oxygen: „ Some microorganism requires oxygen for growth called aerobic. „ Other organism can be inhibited by the presence of oxygen which is called anaerobic. „ Facultative organism can switch the metabolic pathway to allow them to grow under either circumstance. e.g. Saccharomyces cerevisiae. Almost all animals, most fungi and several bacteria are aerobes. Most anaerobic organism are bacteria.
- 10. 11Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Nutrient sources: Microorganism can be classified into two categories on the basis of their carbon sources. „ Heterotrophs use organic compounds such as carbohydrates, lipids, and hydrocarbons as a carbon and energy source. „ Autotrophs use carbon dioxide as a carbon source. e.g. cyanobacteria
- 11. 12Chapter 2 Part I Extremophiles: Organism from those extreme environments. „ Acidophile: An organism with an optimum pH level at or below pH 3. „ Alkaliphile: An organism with optimal growth at pH levels of 9 or above. „ Halophile: An organism requiring at least 0.2M of NaCl for growth. „ Psychrophile: An organism that can thrive at temperatures of 20 °C or lower. „ Thermophile: An organism that can thrive at temperatures between 60-80 °C. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 12. 13Chapter 2 Part I Shape: „ coccus (cocci, pl): A cell with a spherical or elliptical shape. e.g. Streptococcus is a genus of spherical bacteria „ bacillus (bacilli, pl): a cylindrical cell e.g. Bacillus subtilis is a bacterium that is commonly found in soil. „ spirillum (spirilla, pl): a spiral-shaped cell. e.g. Rhodospirillum is a bacterium. Some cells may change shape in response to changes in their local environment. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 13. 14Chapter 2 Part I Section Summary „ Organism cells are highly diverse in terms of their adaptation to the living environment: Temperature, pH, oxygen, moisture, nutrients „ Shapes (bacteria): Coccus, Bacillus and Spirillum JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 14. 15Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 Classification of Cellular Organism (according to cell structure) Cellular Organism Eucaryotes Procaryotes: bacteria Virus Eubacteria: Gram-positive bacteria Gram-negative bacteria Non-gram bacteria: Actinomycetes Cynaobacteria Protists: Fungi, Algae, protozoa Plant: seed plants, mosses Animal: vertabrates and invertabrates Archaebacteria: Methanogen Halogen Thermoacidophiles not free-living organisms Have nuclear membrane and membrane –bound organells? Yes No
- 15. 18Chapter 2 Part I Procaryote „ Procaryotes have no membrane around the cell genetic information and no membrane-bound organelles „ Bacteria: e.g. E. Coli, Rhodospirillum sp. „ Size: 0.5-3µm. „ Grow rapidly: e.g. one cell can replicate into over a million cells in just 12 hours. In contrast, a human cell takes 24 hours to split. „ Utilize carbon sources: carbohydrates, hydrocarbon, protein and CO2. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 16. 19Chapter 2 Part I JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 17. 20Chapter 2 Part I Procaryote Cell Structure „ Nuclear region There is no membrane around the nuclear region containing genetic materials such as chromosomes and DNA (deoxyribonucleic acid). „ Chromosomes: A chromosome is, a very long, continuous piece of DNA, which contains many genes, regulatory elements and other intervening nucleotide sequences. „ The DNA which carries genetic information in biological cells is normally packaged in the chromosomes. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 18. 21Chapter 2 Part I Cytoplasm „ In cytoplasm, there are some visible structures: - ribosomes: sites of protein synthesis, 10,000 per cell, 10 -20 nm, 63% RNA and 37% protein. - storage granules: source of key metabolites, containing polysaccharides, lipids and sulfur granules. Sizes vary between 0.5-1 µm. - Plasmids: DNA molecules separate from the chromosomal DNA and capable of autonomous replication. Usually occur in bacteria. e.g E.coli Application in Genetic Engineering. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 19. 22Chapter 2 Part I „ Cytoplasmic membrane - The cytoplasm is surrounded by a membrane called cytoplasmic membrane. - The cytoplasmic membrane contains 50% protein, 30% lipids and 20% carbohydrates. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 20. 23Chapter 2 Part I „ Cell wall - Eubacteria cell walls contain lipids & peptidoglycan which is a complex polysaccharide with amino acids and forms a structure somewhat like chain- link fence. - Archaebacteria cell walls do not have peptidoglycan. „ Outer membrane: Some bacteria (gram negative cells) have. - To retain important cellular compounds and - To exclude undesirable compounds in the environment. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 21. 24Chapter 2 Part I „ Capsule: Extracellular products can adhere to or become incorporated within the surface of the cell. Certain cells have a coating outside the cell wall called capsule. It contains polysaccharides or polypeptide and forms biofilm response to environmental challenges. „ Pilus (Pili, pl.) A pilus is a hairlike structure on the surface of a cell. Pili enable the transfer of plasmids between the bacteria. An exchanged plasmid can add new functions to a bacterium, e.g., an antibiotic resistance. „ Flagellum: is for cell motion. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 22. 25Chapter 2 Part I Procaryotes Procaryotes include - Eubacteria - Archaebacteria JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 23. 29Chapter 2 Part I Procaryote Reproduction Reproduction: exclusively asexual through binary fission. The chromosome is duplicated and attaches to the cell membrane, and then the cell divides into two equal cells. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 24. 30Chapter 2 Part I Fission JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 25. 32Chapter 2 Part I Eucaryote Cell Structure JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 26. 33Chapter 2 Part I Nucleus „ Nucleus contains chromosomes (DNA associated with small proteins) surrounded by a membrane „ The membrane contains a pair of concentric and porous membrane. Cell wall and membrane structure: „ Eucaryotes contain sterol which strengthen the wall structure and make the membrane less flexible. „ The cell wall of eucaryotes shows variations. e.g. - Fungi contain chitin - Plant cells contain cellulose - Animal cells do not have cell wall so that they are shear - sensitive and fragile. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 27. 34Chapter 2 Part I Membrane-bounded organelles with specialized functions, suspended in the cytoplasm of a eucaryote cell. - Mitichondria are the powerhouses of a eukaryote cell, where respiration takes place. It reduces oxygen and store energy in ATP (Adenosine triphosphate). Shape: Mitochondria have cylindrical shape with 1 µm in diameter and 2- 3 µm in length. - Endoplasmic reticulum is a complex, convoluted membrane system leading from the cell membrane into the cell. The rough endoplasmic reticulum containing ribosomes is the site for protein synthesis. The smooth one is involved with lipid synthesis. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 28. 35Chapter 2 Part I - Lysosomes are very small membrane-bound particles that contain and release digestive enzyme, contributing to digestion of nutrients and invading substances. Enzymes in lysosomes: e.g. Lipases digest lipids. Carbohydrases digest Proteases digest proteins. - Vacuoles are low density and responsible for food digestion, osmotic regulation and waste product storage. - Golgi complexes are small particles composed of membrane aggregates. - Responsible for the secretion of proteins. - Golgi are sites where proteins are modified, important for protein function in the body. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483 http://www.slideshare.net/eplavoi/cells-part-2
- 29. 40Chapter 2 Part I Eucaryotes - Fungi: yeast and mold - Algae Fungi Fungi are heterotrophs which need to take nutrients from the environment for living. „ They are larger than bacteria. Two major groups are yeast and mold. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 30. 41Chapter 2 Part I Yeast Yeasts are very important economically: - Yeasts are responsible for fermentation of beer and bread. (Saccharomyces cerevisiae) - Ethanol production - Wastewater treatment: a mixed culture of yeasts Candida lipolytic Candida tropicalis, and Yarrowia lipolytica grown on hydrocarbons, or gas oil. Yeasts are very important economically: - Yeasts and Bacterium xylinum cultures produce Kombucha, fermented sweetened tea. Yeasts: e.g.Brettanomyces bruxellensis, Candida stellata, Schizosaccharomyces pombe Biochemical Engineering – ChE 483 JUST Department of Chemical Engineering
- 31. 42Chapter 2 Part I Yeast is single-celled. Size: yeasts are 5 to 10 µm in diameter. Shape: spherical, cylindrical or oval. Reproduction: asexual and sexual. „ Asexual reproduction is by either budding or fission. Budding: a small bud cell forms on the cell, which gradually enlarge and separate from the mother cells. Most of the yeasts reproduce by budding. Baker’s yeast, Saccharomyces cerevisiae. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 32. 45Chapter 2 Part I Molds Molds are filamentous fungi and have a mycelial structure. • Mycelium is highly branched system of tubes that contains mobile cytoplasm with many nuclei. • Hypha is long, thin filaments on the mycelium. „ Molds are very important economically: - mushroom farming is a large industry in many countries. Agaricus bisporus JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 33. 46Chapter 2 Part I Size: „ When grow on solid surface, the filamentous form is 5-20 µm. „ When grow in submerge culture, it can form aggregates and pellets, 50 µm-1mm. - Cause nutrient transfer problem in the pellet JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 34. 48Chapter 2 Part I Eucaryote-Algae Algae are usually unicellular or plantlike multicellular organism. „ Like plants, most algae use the energy of sunlight to make their own food, a process called photosynthesis. „ Algae lack the roots, leaves, and other structures typical of true plants. „ Algae contain chloroplast which is responsible for photosynthesis. „ Unicellular algae are considered in Microbiology „ E.g. Chlorophyta, Chrysophyta (brown, yellow-green algae) „ They are in the size of 10-30 µm. „ Algae can reproduce asexually or sexually. Many of algae incorporate both sexual and asexual modes of reproduction. „ Algae contain alginic acid and agar. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 35. 49Chapter 2 Part I Virus „ Not free-living organisms, obligate parasite of other living cells. „ Size: 30-200 nm. „ Can not capture or store free energy. „ Not functionally active except when inside their host cells. „ Can do harm but also be useful biotechnology tools (e.g. vaccines). „ Bacteriophage or phage: virus infecting bacteria. „ (Virus: virus infecting eukaryotes) „ Virus reproduction: - Virus contains genetic materials such as DNA and RNA which is covered by a protein coat called capsid. - They can reproduce only by invading and controlling other cells as they lack the cellular machinery for self-reproduction. JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 36. 51Chapter 2 Part I Section Summary „ Organism cells are highly diverse in terms of their adaptation to the living environment: „ Temperature, pH, oxygen, moisture, nutrients „ Shapes (bacteria): Coccus, Bacillus and Spirillum Primary Classification Cellular Organism Eucaryotes Procaryotes Virus not free-living organisms Have nuclear membrane and membrane-bound organelles? Yes No JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 37. 53Chapter 2 Part I Primary Classification Cellular Organism Eucaryotes Procaryotes Virus not free-living organisms Have nuclear membrane and membrane-bound organelles? Yes No Cytoplasmic granules: - Ribosome: protein synthesis - Storage granules: source of key metabolites, including polysaccharides, lipids and sulfur granules. - Capsule - Pili - Flagella Eubacteria: gram-positive, gram-negative, non-gram, actinomycetes and cyanobacteria Archaebactria: methanogen Halogen thermoacidophiles Mostly asexual reproduction JUST Department of Chemical Engineering Biochemical Engineering – ChE 483
- 38. 54Chapter 2 Part I Primary Classification Cellular Organism Eucaryotes Procaryotes Virus: reproduce in the host cell Eubacteria: Gram-positive bacteria Gram-negative bacteria Non-gram bacteria Actinomycetes Cynaobacteria Fungi: yeast, mold Algae: Reproduction: asexual or sexual Archaebateria: methanogen Halogen Thermoacidophiles not free-living organisms Have nuclear membrane and membrane-bound organelles? Yes No Asexual reproduction JUST Department of Chemical Engineering Biochemical Engineering – ChE 483