Microbiology 微生物学 Spring-Summer
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1 Microbiology 微生物学 2014 Spring-Summer
2 Microbiology 微生物学 2017 Spring-Summer
3 Relevant Information and Resources Course slides can be found at 教学工作 Course-related questions will be answered through s. Textbook: Brock Biology of Microorganisms (13 th )
4 Chapter 2 A brief Journey to the Microbial World
5 Chapter 2: Microbial World II Cell structure and Evolutionary history 2.5 Elements of Microbial structure (Discuss later in Chapter 4 and 10) 2.6 Arrangement of DNA in Microbial Cells (Discuss later in Chapter 11) 2.7 The Evolutionary Tree of Life (Discuss later in Chapter 14)
6 An Eukaryotic Cell Cytoplasmic membrane Endoplasmic reticulum Ribosomes Nucleus Nucleolus Nuclear membrane Golgi complex Cytoplasm Mitochondrion Chloroplast Eukaryote
7 A Prokaryotic Cell Cytoplasm Nucleoid Ribosomes Plasmid Cell wall Prokaryote Cytoplasmic membrane
8 Evolutionary history Keep in Mind: The word prokaryote should not be considered synonymous with primitive, as all cells living today whether prokaryotes or eukaryotes are highly evolved and closely adapted to their habitat.
9 Arrangement of DNA Nucleus vs Nucleoid Eukaryote Prokaryotes Cytoplasmic membrane Nucleus Nucleoid Cell wall Eukarya Mitochondrion
10 Arrangement of DNA E. coli a) DNA is stained to show nucleoid. b) DNA is released from a disrupted cell
11 Evolutionary Tree of Life DNA Cells Gene encoding ribosomal RNA DNA sequencing Aligned rrna gene sequences Isolate DNA PCR Sequence analysis Generate phylogenetic tree
12 Evolutionary Tree of life BACTERIA ARCHAEA EUKARYA Flavobacteria Green nonsulfur bacteria Mitochondrion Gram- Proteobacteria positive bacteria Chloroplast Cyanobacteria Crenarchaetoa Thermoproteus Pyrodictium Marine Crenarchaeota Thermococcus Methanobacterium Methanococcus Pyrolobus Euryarchaeota Methanosarcina Thermoplasma Methanopyrus Entamoebae Extreme halophiles Slime molds Animals Fungi Plants Ciliates Flagellates Trichomonads Thermotoga Thermodesulfobacterium Aquifex LUCA Diplomonads (Giardia) Microsporidia LUCA Last Universal Common Ancestor
13 Chapter 2: Microbial World III Microbial Diversity 2.8 Metabolic Diversity (Discuss later in Unit V) 2.9 Bacteria (Discuss later in Chapter 11) 2.10 Archaea (Discuss later in Chapter 14) 2.11 Communities 2.12 Eukarya
14 Microbial Diversity Micro-organ-isms: Diverse Structure Living Carbon Energy Light Hetero Auto Organic Inorganic
15 Metabolic Diversity Energy: PHOTOTROPHS (use light as energy source) Carbon: CO 2 Organic C Photoautotrophs Photoheterotrophs Heterotroph: Carbon source is NOT CO 2 ; Autotroph: Carbon source is CO 2 ;
16 Metabolic Diversity Energy Sources Chemicals Light Aerobe: with oxygen; Organic chemicals (glucose, acetate, etc.) Chemotrophy Chemoorganotrophs Inorganic chemicals (H 2, H 2 S, Fe 2+, NH 4+, etc.) Phototrophy Chemolithotrophs Phototrophs (glucose O 2 CO 2 H 2 O) (H 2 O 2 H 2 O) (light) Anaerobe: without oxygen; Facultative: with or without oxygen; Only In Prokaryotes
17 Metabolic Diversity Anoxygenic Reducing power Carbon electrons Energy hv Anoxygenic : producing no oxygen Oxygenic Reducing power Carbon Energy hv hv Evolution Oxygenic: producing oxygen;
18 Metabolic Diversity Phototrophic and chemolithotrophic proteobacteria (a) The phototrophic purple sulfur bacterium, Chromatium; (b) The chemolithotrophic sulfur-oxidizing bacterium, Achromatium
19 Bacteria Spirochetes Thermotoga Deinococcus Green nonsulfur bacteria OP2 Green sulfur bacteria Planctomyces Chlamydia Cyanobacteria Gram-positive bacteria Aquifex Proteobacteria Mitochondrion Phylogenetic tree of Bacteria
20 Bacteria Gram-negative Bacteria (Proteobacteria, the largest division of bacterial domain): Escherichia coli, Pseudomonas, Azotobacter, Salmonella,
21 Bacteria Gram-positive Bacteria: Bacillus (left), Clostridium, Streptomyces (Right), Mycoplasma (Lacking a cell wall)
22 Bacteria Gram-positive Bacteria: Bacillus (left), Clostridium, Streptomyces (Right), Mycoplasma (Lacking a cell wall)
23 Bacteria Cyanobacteria (Gramnegative)
24 Bacteria Planctomyces (Gram-staining?) having some features of eukaryotes Spirochetes (Gram-negative) Chlamydia Deinococcus (Gram-positive)
25 Bacteria Phototrophic green bacteria: (a) Chlorobium (green sulfur bacteria) (b) Chloroflexus (green non-sulfur bacteria) possible first phototrophic bacteria on Earth Hyperthermophile: Aquifex (Gramnegative)
26 Archaea Marine group Halobacterium Natronobacterium Euryarchaeota Crenarchaeota Marine group Sulfolobus Halophilic methanogens Methanobacterium Methanocaldococcus Methanosarcina Thermoplasma Thermoproteus Pyrococcus Pyrolobus Methanopyrus Desulfurococcus Hyperthermophiles Phylogenetic tree of Archaea. Hyperthermophiles (circled), Methanogens and halophiles/acidophiles
27 Archaea Pyrolobus (hyperthermophile) Thermoplasma (extremely acidophilic)
28 Communities Biofilm (single species) Biofilm (Multispecies)
29 Eukaryotic Microorganisms Flagellates Diplomonads Trichomonads Slime molds Ciliates Animals Diatoms Brown algae Early-branching, lack mitochondria Phylogenetic tree of Eukarya. Green algae Plants Red algae Fungi
30 Eukaryotes Microbial Eukarya that do NOT have mitochondria Diplomonads,Giardia lamblia Trichomonads, Trichomonas vaginalis
31 Eukaryotes Microbial Eukarya. (a) Algae,Volvox; (b) Fungi, the sporebearing structure of a typical mold; (c) Protozoa, the ciliated protozoan Paramecium
32 Eukaryotes Microbial Eukarya. Slime mold, Physarum Microbial Eukarya. Lichens, a fungus and a phototrophic organism (algae or cyanobacterium);
33 Eukaryotes fungi (Chapter ) Chytridiomycetes Zygomycetes Glomeromycetes Ascomycetes Saccharomyces cerevisiae; Beauveria; Metarhizium Basidiomycetes
34 Eukaryotes fungi (Chapter ) Fungal structure and growth
35 Eukayotes fungi (Chapter ) Saccharomyces cerevisiae (a) Colonies of Aspergilus species; (b) Conidiophore and conidia of Aspergillus fumigatus
36 Eukaryotes fungi (Chapter ) Life cycle of a typical ascomycetes, Saccharomyces cerevisiae
37 Chapter X Chemistry of Cellular Components
38 Chemical Bonds Ethylene, a double-bonded organic compound Acetylene, a triple-bonded organic compound Carbon dioxide Nitrogen Phosphate Peptide bond of proteins Cytosine (nitrogen base of DNA and RNA) Phenylalanine (amino acid in proteins)
39 Chemical Bonds Amino terminus Water Cytosine Amino acids in a protein Guanine Thymine Adenine Hydrogen bonds Nitrogen bases in DNA
40
41 Chemical Bonds
42 Macromolecules Flagellum Cytoplasmic membrane Cell wall Cytoplasm Proteins Nucleoid Ribosomes Nucleic Acids:DNA RNA Polysaccharides Storage granules Lipids
43 Sugars and Polysaccharides Sugar Open chain Ring Significance Pentoses Ribose Backbone of RNA -1,4-Glycosidic bond Deoxyribose Backbone of DNA -1,6-Glycosidic bond -1,4-Glycosidic bond Hexoses Glucose Energy source; cell walls Starch -1,4 bonds -1,6 bonds Fructose Energy source; fruit sugar Glycogen Cellulose -1,4 bonds -1,4 bonds
44 Lipids Common fatty acids: C 16 saturated (palmitic) Simple lipids (triglycerides): Fatty acids linked to glycerol by ester linkage Glycerol C 16 monounsaturated (palmitoleic) Fatty acids Ester linkage Complex lipid: Phosphatidyl ethanolamine (a phospholipid) Complex lipid: Monogalactosyl diglyceride (a glycolipid) Fatty acids Phosphate Ethanolamine Galactose Fatty acids
45 Amino acids and Proteins -carbon Amino group General structure of an amino acid Ser Serine (S) Carboxylic acid group Asp Aspartate (D) Glu Glutamate (E) Lys Lysine (K) Pyl Pyrrolysine (O) Gly Glycine (G) Ala Alanine (A) Val Valine (V) Leu Leucine (L) Ile Isoleucine (I) Thr Threonine (T) Asn Asparagine (N) Gln Glutamine (Q) Arg Arginine (R) His Histidine (H) Met Methionine (M) Phe Phenylalanine (F) Trp Tryptophan (W) Cys Cysteine (C) Sec Selenocysteine (U) Tyr Tyrosine (Y) Structure of the amino acid R groups Key Ionizable: acidic Ionizable: basic Nonionizable polar Nonpolar (hydrophobic) Pro Proline (P) (Note: Because proline lacks a free amino group, the entire structure of this amino acid is shown, not just the R group.
46 Amino acids and Proteins rrna for UAG Selenocysteine: UGA Pyrrolysin: UAG
47 Amino acids and Proteins a a d C b b C d c c D-Glucose L-Glucose L-Alanine D-Alanine N-terminus C-terminus Peptide bond Three-dimensional projection Peptide Bond formation Isomers
48 Amino acids and Proteins Hydrogen bonds between nearby amino acids -helix -sheet Hydrogen bonds between distant amino acids Secondary Structure of Polypeptides
49 Amino acids and Proteins A chain -helix -sheet B chain Tertiary Structure of Polypeptides Insulin Ribonuclease Chains Chains Quaternary Structure of Polypeptides Chains Chains
50 Amino acids and Proteins Denaturation of the protein ribonuclease Gentle denaturation; urea Active protein Harsh denaturation; 100 C Inactive Inactive Remove urea; reactivation Cool Active protein Inactive
51 Nucleic acids, DNA, and RNA Pyrimidine bases Purine bases Phosphate Base Nucleotides Phosphoanhydride Phosphates Phosphate ester Ribose Ribose H only in DNA Cytosine (C) DNA RNA Adenine Thymine (T) DNA only Uracil (U) RNA only Adenine (A) DNA RNA Guanine (G) Structure of the nitrogen bases of DNA and RNA DNA RNA Components of the important nucleotide, Adenosine TriPhosphate (ATP)
52 Nucleic acids, DNA, and RNA 5 position Base Nitrogen base attached to 1 position Hydrogen bonds 3 position Deoxyribose (i) Phosphodiester bond Base (ii) Primary structure Region of complementary base pairing Secondary structure Structure of part of a DNA chain DNA and RNA
53 Chapter 3 Cell Structure and Function in Bacteria and Archaea
54 Size of Living Things
55 Cell Shape and Size
56 Cell Shape and Size
57 Cell Shape and Size A giant prokaryote, the surgeonfish symbiont: Epulopiscium fishelsoni 600 um long and 75 um wide with three eukaryote paramecium The largest prokaryote, Thiomargarita namibiensis 400 um wide.
58 Cell Shape and Size r = 1 µm r = 2 µm r = 1 µm Surface area (4πr 2 ) = 12.6 µm Volume ( πr 3 ) = 4.2 µm 3 Surface Volume = 3 r = 2 µm Surface area = 50.3 µm 2 Volume = 33.5 µm 3 Surface Volume = 1.5 Space for essential biomolecules Nutrient uptake rate metabolism rate Evolution: more cells more mutations more possibilities Haploid Diploid 0.15 µm < independent living cells < 750 µm
59 Cell Structure Prokaryote Eukaryote
60 Cell Structure Prokaryotes Eukaryote Cytoplasmic membrane Nucleus Bacteria Archaea Cell wall Eukarya Mitochondrion
61 Cytoplasmic Membrane Hydrophilic region Hydrophobic region Fatty acids Hydrophilic region Glycerol Phosphate General chemical structure of phospholipid Glycerophosphates Fatty acids TEM of a membrane from Halorhodospira halochloris H-bonds & hydrophobic interactions Mg 2+, Ca 2+, + phospholipids ionic bonds
62 Cytoplasmic Membrane 6 8 nm Phospholipids Out Hydrophilic groups Hydrophobic groups Integral membrane proteins In Phospholipid molecule Sterols in eukaryotes Integral One-end inserted Peripheral Unevenly distributed functionally clustered Rigidity agents Hopanoids in bacteria, missing in Archaea
63 Cytoplasmic Membrane General structure of lipids in Archaea 6 8 nm Phospholipids Out In Hydrophilic groups Hydrophobic groups Integral membrane proteins Phospholipid molecule a. Eukaryote and Bacteria; b. Archaea; Ester or ether? Fatty acids or repeated isoprene c. Isoprene
64 Cytoplasmic Membrane Major lipids of Archaea and the structure of archaeal cytoplasmic membranes Ether linkage Phytanyl Isoprene unit Glycerol diether CH 3 groups Isoprene unit Extremely resistant to heat Biphytanyl Diglycerol tetraethers
65 Cytoplasmic Membrane Major lipids of Archaea and the structure of archaeal cytoplasmic membranes Crenarchaeol Out Out Glycerophosphates Phytanyl Membrane protein Biphytanyl In In Lipid bilayer Lipid monolayer
66 Cytoplasmic Membrane - Function 1. Permeability Barrier Prevents leakage and functions as a gateway for transport of nutrients into and out of the cell 2. Protein Anchor Site of many proteins involved in transport, bioenergetics, and chemotaxis 3. Energy Conservation Site of generation and use of the proton motive force
67 Cytoplasmic Membrane Even for water, specific transport proteins (aquaporins) are needed in certain cases.
68 Rate of solute entry Cytoplasmic Membrane Transporters versus diffusion Transporter saturated with substrate Transport Simple diffusion Characteristics of Transport Proteins: 1. Saturation effect; 2. High specificity; 3. Tightly regulated External concentration of solute
69 Transport and transport systems Simple transport: Driven by the energy in the proton motive force Out In Phosphoanhydride Phosphate ester Ribose Transported substance Group translocation: Chemical modification of the transported substance driven by phosphoenolpyruvate 1 ABC transporter: Periplasmic binding proteins are involved and energy comes from ATP 2 3 Phosphates Adenosine TriPhosphate (ATP) Adenine The three classes of membrane transport systems
70 Transport and transport systems Out In Uniporter Antiporter Symporter Structure of membrane-spanning transporters and types of transport events
71 Simple transport Out In Sulfate symporter Potassium uniporter Phosphate symporter Sodium-proton antiporter Lac permease (a symporter) Function of the Lac permease symporter of Escherichia coli and several other wellcharacterized simple transporters
72 Group translocation Glucose Cytoplasmic membrane Out PE Pyruvate Nonspecific components Enz HPr Specific components Enz II a Enz II b Enz II C Direction of glucose transport Direction of P transfer In Glucose 6 P Mechanism of the phosphotransferase system of Escherichia coli Phosphoenolpyruvate (PEP) Pyruvate
73 ABC system Peptidoglycan Periplasm Out Periplasmic binding protein Transported substance ABC: ATP-binding cassette Membranespanning transporter In ATPhydrolyzing protein Mechanism of an ABC transporter
74 Protein Secretion System
75 Protein Secretion System-Sec
76 Protein Secretion System
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