General aspects of bacteriology, bacterial structure and growth. Che-Hsin Lee, Ph.D. Department of Biological Sciences National Sun Yat-senUniversity

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1 General aspects of bacteriology, bacterial structure and growth Che-Hsin Lee, Ph.D. Department of Biological Sciences National Sun Yat-senUniversity 1

2 Human Microbiome Project Providing metabolic function Stimulating immunity Preventing with unwanted pathogens 2

3 Intestinal microbiota protection against enteric infections 3

4 Effect of antibiotics on the gut microbiota 4

5 Gut microbiota regulates blood pressure Nature Reviews Cardiology 5

6 Robert Koch Infectious diseases are caused by microorganisms, each one responsible for a particular disease Disease caused by a community of organisms rather than a single species of bacteria. 6

7 Probiotics and prebiotics Probiotics are commonly gram-positive bacteria (e.g. Bifidobacterium, Lactobacillus) and yeasts (e.g. Saccharomyces). Yogurt and Kefir. Although probiotics are safe dietary supplement, not all probiotics are effective and for all people. Prebiotics: the use of metabolic supplements promote a healthy microbiota (e.g. fiber, fructo-oligosaccharide) Symbiotics: Probiotics + prebiotics 7

8 Sterilization Total destruction of all microbes 8

9 Disinfection Destroy most microbial form 9

10 Antiseptic agents Reduce the number of microbes 10

11 Properties of disinfectants and antiseptic agents 11

12 Differences between eukaryotes and prokaryotes 12

13 Differences between eukaryotes and prokaryotes 13

14 Bacterial cell walls 14

15 Gram stain 15

16 Bacterial morphology 16

17 Gram-positive and gram-negative bacteria 17

18 Functions of the bacterial envelope 18

19 Membrane characteristics of Gram-positive and Gramnegative bacteria 19

20 Structure of the peptidoglycan 20

21 Peptidoglycan synthesis 21

22 Teichoic acid 22

23 Lipopolysaccharide (LPS) 23

24 Lipopolysaccharide (LPS) 24

25 Cell division 25

26 Structure of the spore 26

27 Sporogenesis 27

28 Bacterial metabolism, growth, and genetics

29 Outline Metabolism and the conversion of energy Biosynthesis DNA Transcriptional control Mutation, repair, and recombination

30 Oxygen (O 2 ) Obligate anaerobes Obligate aerobes Facultative anaerobes

31 Catabolism Anabolism Intermediary metabolism

32 Glycolytic pathway (Embden- Meyerhof-Parnas pathway) Nicotinamide adenine dinuceotide (NADH)

33 Fermentation

34 Tricarboxylic acid (TCA) cycle

35 Fermentation an aerobic metabolism Fermentation: 2 ATP molecules per glucose Aerobic metabolism with electron transport: 38 ATP per glucose

36 Aerobic glucose metabolism

37 TCA cycle 1. It is the most efficient mechanism for the generation of ATP. 2. It serves as the final common pathway for the complete oxidation of amino acids, fatty acids, and carbohydrates. 3. It supplies key intermediates for the ultimate synthesis of amino acids, lipids, purines, and pyrimidines. The last two functions make the TCA cycle a so-called amphibolic cycle.

38 Genes and expression instruct.westvalley.edu/svenssoncellsandgenes/10molecularbiology.html

39 Transcription instruct.westvalley.edu/svenssoncellsandgenes/10molecularbiology.html

40 Genetic code UUU UCU UAU UGU UUC Phe UCC Ser UAC Tyr UGC Cys UUA UCA UAA Stop UGA Stop UUG Leu UCG UAG Stop UGG Trp CUU CCU CAU CGU CUC Leu CCC Pro CAC His CGC Arg CUA CCA CAA CGA CUG CCG CAG Gln CGG AUU ACU AAU AGU AUC Ile ACC Thr AAC Asn AGC Ser AUA ACA AAA AGA AUG Met ACG AAG Lys AGG Arg GUU GCU GAU GGU GUC Val GCC Ala GAC Asp GGC Gly GUA GCA GAA GGA GUG GCG GAG Glu GGG

41 Bacterial protein synthesis

42 Control of gene expression: the lactose operon P: promoter I: Repressor O: Operator Z:β-galactosidase Y: permease A: acetylase

43 Replication of DNA Helicase Primase DNA-dependent DNA polymerase Semiconservatively 5 to 3 Okazaki fragments Topoisomerase

44 Bacterial cell division

45 Phases of bacterial growth Log phase

46 Mutations Transition: one purine is replaced by another purine Transversion: one purine is replaced by one pyrimidine Silent mutation: amino acid is not changed Missense mutation: different amino acid Conservative mutation: the new amino acid has similar properties Nonsense mutation: amino acid stop codon Frameshift mutation: change in the reading frame Null mutations: completely destroy gene function Purine: Adenine (A) Guanine (G) Pyrimidine: Cytosine (C) Thymine (T) Uracil (U)

47 Repair mechanisms of DNA Direct DNA repair Excision repair Recombinational repair SOS response (Error-prone repair)

48 Gene exchange in bacteria Plasmid Bacteriophages Transposons

49 Transposons

50 Mechanisms of genetic transfer between cells Conjugation Transformation Transduction Transposon

51 Generation of drug-resistant Staphylococcus aureus by multiple genetic manipulations

52 Cloning

53 Viral classification, structure, and replication

54 Viruses

55 Viruses

56 Viruses

57 Components of the basic virion

58 Viruses

59 The DNA viruses and their morphology

60 The RNA viruses, their genome structure, and their morphology

61 Naked capsid virus and Enveloped virus

62 Virion structure: Naked capsid

63 Virion structure: Envelope

64 Icosahedral capsid of a picornavirus

65 Cryoelectron microscopy and computergenerated 3D image reconstructions of icosahedral caspids

66 The hemagglutinin glycoprotein trimer of influenza A virus

67 Viral replication

68 Steps in viral replication

69 Single-cycle growth curve for a virus

70 Viral attachment proteins

71 Viral receptors

72 Viral macromolecular synthesis steps

73 Mechanisms of viral pathogenesis

74 Viral disease

75 The stages of viral infection

76 Progression of viral disease

77 Determinants of viral pathogenesis I

78 Determinants of viral pathogenesis II

79 Determinants of viral pathogenesis III

80 Types of viral infections at cellular level

81 Mechanisms of viral cytopathogenesis I

82 Mechanisms of viral cytopathogenesis II

83 Mechanisms of viral transformation and immortalization

84 Viral immunopathogenesis

85 Viral infection

86 Incubation periods of common viral infections I

87 Incubation periods of common viral infections I

88 Viral transmission

89 Role of viruses in disease

90 Major target tissues of viral disease

91 Oral and respiratory diseases I

92 Oral and respiratory diseases II

93 Oral and respiratory diseases III

94 Gastrointestinal viruses

95 Viruses transmitted in blood

96 Sexually transmitted virus

97 Screening of the blood supply

98 Arboviruses and Zoonoses

99 Laboratory diagnosis of viral disease

100 Laboratory procedures for diagnosing viral infections

101 Cytology Syncytium formation by measles virus Cytopathologic effect by HSV Negri bodies caused by rabies

102 Viral cytopathologic effects

103 Systems for propagation of viruses

104 Titer

105 HA and HI test

106 Western blot analysis

107 Antiviral agents and infection control

108 Viruses treatable with antiviral drugs Picornavirus

109 Examples of targets for antiviral drugs I

110 Thank you for your attention!!

Bacterial Gene Finding CMSC 423

Bacterial Gene Finding CMSC 423 Finding Signals in DNA We just have a long string of A, C, G, Ts. How can we find the signals encoded in it? Suppose you encountered a language you didn t know. How would