M122 Microbiology MIDTERM REVIEW

1. Tutors: Suleiman Saroia (M, W 10-11am Nat Sci 2108) Amy Vanmali (M,W 11-12am Nat Sci 2108) M122 Microbiology MIDTERM REVIEW

2. The Basics • Microbiology is the study of microorganisms • A pathogen is a microbe that causes disease. • Normal flora don't cause disease and therefore are non-pathogenic • E. Coli in our intestines • S. Aureus on our skin • HOWEVER: in immunocompromised people (i.e. AIDS) non-pathogenic microbes can become pathogenic when unregulated! • Germ Theory - the theory that diseases are caused by germs (microbes)

3. Impact on Humans: legumes ruminants Earth’s life support:agriculture, energy and environment

4. Important people and Discoveries of/regarding Microorganisms Antony von Leeuwenhoek- The first to accurately describe microoraganisms (discovered bacteria/protozoa) Robert Hooke -First to publish description about microorganism(discovered fruiting mold) Luis Pasteur - Proved biogenesis for microorganisms. FranscescoRedi-Proved biogenesis for large organisms. Robert Koch- Was the first to establish relation between bacteria and disease (Germ Theory) Carl Woese - Used rRNA sequencing which led to discovery of archaea.

5. Spontaneous Generation vs. Biogenesis  Definition of Spontaneous Generation: Life arises spontaneously from non-living matter •  Definition of Biogenesis: • Life arises from pre-existing life • PROOF: • Large organisms: Redi “maggot experiment” • Microorganisms: Pasteur “Swan Neck Flask”

6. Redi's Maggot Experiment

7. Conclusion of Redi’s Maggot Experiment • Conclusion: • - Rotting meat does not spontaneously produce maggots. • - Maggots form only when flies are present, i.e. flies carry eggs of maggots.

9. No Spontaneous Generation of Microorganism !

10. Robert Koch • Demonstrated the Role of Bacteria in Causing Diseases via • “Koch’s Postulates” • The microbe must only be present in infected organism, not in a healthy animals blood. • 2. Isolate the microbe, and grow it in pure culture . • 3. Take isolated microbe and inject into a healthy organism(should develop same signs and symptoms) • 4. Re-isolate the microbe from healthy organism and should be same as the original microbe.

11. Observe pathogenic organism Culture pathogenic organism Inject pathogenic organism Recover pathogenic organism

12. Importance of Koch’s Work • Developed pure culture methods: • - growth on solid media • - isolation of pure cultures • (like in micro lab …Word.) • Scientific method to prove causation of disease • EX)*(established the link between bacillus anthracis (bacteria) anthrax (disease).

13. What is a cell? Basic unit of all cellular life • organisms can be cellular or acellular • Cells are enclosed by a sort of barrier (cell wall or cell membrane) • -Cellular cells include to main types: • - prokaryotes (bacteria, archae) • -eukaryotes (fungi, protists, algae) • … almost everything is cellular except • VIRUSES ARE ACELLULAR

14. Basic Properties of Cells • 6 Basic Properties of Cells: • 1) Metabolism (anabolism/catabolism) • 2) Reproduction (grow) • 3) Locomotion (movement) • 4) Differentiation • 5) Communication • 6) Evolve

15. Eukaryotes - 80S ribosomes (40s+60s) - Nucleus - membrane-bound organelles (i.e. mitochondria, golgi, ER, etc.) Prokaryotes vs. Eukaryotes Prokaryotes - 70S ribosomes (30s+50s) - NO nucleus - NO membrane bound organelles Note: prokaryotic cells are typically smaller than eukaryotic cells.

16. Bacteria - have peptidoglycan in cell wall composition - simple shapes like round, rod, etc. Prokaryotes (Archae vs. Bacteria) Archae - cell wall composition is more complex - seen as having both bacterial/eukaryote characteristics! - live in extreme environments (*Streptomycesthermoautotrophicus– thermophile) *REMEMBER: Archae was discovered by Carl Woese who compared rRNA sequences

17. Eukaryotes(Protozoa, Fungi, Algae) Protozoa Fungi Plants • Single-celled single/multi celled single/multi celled • No cell walls have cell walls have cell walls • Motile No photosyn. pigments Photosynthesis • Aquatic environments • Part of food chain • Some are pathogens

18. Acellular microorganisms: Viruses Characteristics: A Major class of microorganism Not cellular Made of nucleic acid + protein Obligate intracellular parasites

19. An organism is found to live in a lake which is found to have 5M NaCl. This is known to be a salinity in which most microorganisms cannot survive. This microorganism is most likely: a. bacteria b. archae c. protist d. fungi e. all of the above

20. An organism is found to live in a lake which is found to have 5M NaCl. This is known to be a salinity in which most microorganisms cannot survive. This microorganism is most likely: a. bacteria b. archae c. protist d. fungi e. all of the above

21. An organism is found to have peptidoglycan cell wall composition. Which of the following statements is true? a. It is bacteria, and has 70S ribosomes b. It is bacteria, and has 80S ribosomes c. It is archae, and has 70S ribosomes d. It is archae, and has 80S ribosomes e. none of the above are true statements

22. An organism is found to have peptidoglycan cell wall composition. Which of the following statements is true? a. It is bacteria, and has 70S ribosomes b. It is bacteria, and has 80S ribosomes c. It is archae, and has 70S ribosomes d. It is archae, and has 80S ribosomes e. none of the above are true statements

23. Lecture 2Prokaryotes

24. Typical Prokaryotic Cell Typical Eukaryotic Cell Plasma Membrane “Open”Nucleoid Mitochondria & Chloroplasts Membrane-enclosed Nucleus

25. Prokaryotic Cell Sizes • Typical Sizes: • Width - 1-2 m • Length - 2-10 m long • Exceptions: • “Nanobacteria” - less than 0.2 m • A few large bacteria - up to 750 m

26. Sizes of Bacteria and Viruses Cyanobacterium Smallest bacteria are about the size of the largest viruses

27. Epulopisciumfishelsoni Comparable to the size of a printed hyphen Thiomargarita namibiensis(white sphere) is comparable in size to the head of a fruit fly.PRETTY BIG

28. Prokaryotic Cell Shapes Bacillus

29. Hypha e.g. Streptomyces (fungus-like bacteria) Function  Supports & protects the cells. Stalk e.g. Caulobacter Contains cytoplasmic material that is devoid of ribosomes and DNA. Function  Maybe in nutrient absorption.

30. Spherical (Cocci) Bacteria: Diplo – pairs Staphylo – grape-like clusters Strepto – chain Tetrads – groups of 4 Sarcinae – groups of 8

31. Spiral Bacteria:Vibrio, Spirilla, Spirochete • Vibrios - curved rods • Spirilla - 2 or more twists • Spirochetes - corkscrew shaped

32. Prokaryotic Structure: Plasma or Cell Membrane Fimbra/Pilus

33. Amphipathic Plasma Membrane Composed of: • Phospholipidbilayerasymmetric  polar & nonpolarend • Membrane proteins=integral & peripheral protein) • Hopanoids - embedded in bilayer • Sterol-like (similar to cholesterol) which stabilize membrane • Stabilize membrane Amphipathic

34. Structure of Plasma Membrane: Floating in a lipid bilayer Hydrophobic fatty acid chains Hydrophilic ends of the membrane phospholipids Loosely associated with the inner membrane surface “Fluid Mosaic Model of Bacterial Membrane Structure”

35. Components Phospholipids Hopanoids Integral Proteins Peripheral Proteins Plasma Membrane Functions • Separates cell • Selectively permeable • Location of metabolic reactions • Responds to surroundings • Chemotaxis

36. Internal Membrane System Mesosomes: • invaginations of plasma membrane • Artifacts of chemical fixation Complex in-foldings of plasma membrane: • Usually in photosynthetic or other prokaryotes with high respiratory activity • Vesicles or tubular membranes

37. Cytoplasm • 70 % water • Thick / Elastic • Has ribosomes and inclusion bodies • Highly organized with respect to protein location

38. Inclusion Bodies • Structure: made of organic or inorganic materials • Function: nutrient & energy storage; others • Examples: • poly-b-hydroxybutyrate: phosphate storage. Plastics! • Alcaligenes eutrophus • gas vacuoles: provide buoyancy • Cyanobacterium • magnetosome: iron containing, orientation in magnetic field • Magnetospirillum magnetotacticum

39. Ribosomes/Nucleoid Ribosomes • ribosomal RNA (rRNA) + protein • Site of protein synthesis • 70S Nucleoid • Irregularly shaped region, containing bacterial chromosome

40. Plasmids • Extra-chromosomal DNA • Small, circular “mini-chromosomes” • Function: • Extra info: NOT required for growth • May provide antibiotic resistance • Transferrable between bacteria via conjugation

41. Cell Wall • Gives shape / support • Protects from osmosis lysis and toxins • Made of peptidoglycan (murein)

42. Peptidoglycan Formed by identical subunits Alternating NAG/NAM form sugar chains

43. Peptidoglycan • N-acetyl-glucosamine • (NAG) • N-acetyl-muramic acid • (NAM) Tetrapeptide side chain composed of alternating D- and L-amino acids (these D-amino acids are not found in proteins) The peptidoglycan “subunit” of Escherichia coli

44. Peptidoglycan Cross-Links Direct cross-linking Gram NEGATIVE = DIRECT Diaminopimelic acid Peptide interbridge Gram POSITIVE=PEPTIDE INTERBRIDGE

45. All cells purple All cells purple G+ = purple, G- = colorless G+ = purple, G- = red/pink Gram Staining 1.) Crystal violet for 1 min 2.) Iodine for 3 min 3.) Add alcohol (decolorizer) 4.) Safranin for 1-2 min

46. Gram + • No outer membrane • Peptidoglycan layer is thick • Has Teichoic Acid • Periplasmic Space is thin • Sensitive to Penicillin • Flagella has two rings (inner and outer)

47. Gram - • Has outer membrane • Peptidoglycan is thin • Has LPS • Penicillin resistant • Periplasmic space is thick • Flagella has 4 rings (LPSM)

48. Outer Membrane for G- • Another barrier for transport • Protects from antibiotics and digestive enzymes • Has porin proteins • More permeable than inner membrane • Is strengthened by Braun’s lipoprotein

49. Periplasmic Space • Thin in G+ bacteria • Contains exoenzymes • Thick in G- bacteria • Peptidoglycan synthesis • Nutrient acquisition • Modifies toxins

50. Teichoic Acid and LPS • Both are antigens that give negative charges • Techoic (G +) • LPS (G -) • LPS stabilizes membrane (contains anO-side chain recognized by antibodies, core polysaccharide, lipid A) • LPS can act as an endotoxin