BIOL 4501   GENERAL MICROBIOLOGY    Fall 1999

I. CELL TYPES

A. Eukaryotic Cells
B. Prokaryotic Cells

II. CYTOPLASMIC MEMBRANE

A. Structure - Fluid Mosaic Model
B. Internal Membranes in Prokaryotes
C. Function of Cytoplasmic Membrane

III. MOVEMENT OF MOLECULES THROUGH MEMBRANES

A. Transport Proteins
B. Cytosis
C. Diffusion
D. Active Transport
E. Group Translocation

 

I. EUBACTERIA

A. Gram Negative Bacteria
B. Gram Positive Bacteria
C. Biosynthesis of Peptidoglycan
D. Mycoplasmas

II. ARCHAEBACTERIA

A. Do Not Contain Muramic Acid or D-Amino Acids
B. Several Types of Cell Walls Have Been Found

III. EUKARYOTES

A. Fungi
B. Algae
C. Protozoa

 

I. PROKARYOTIC CELLS

A. Bacterial Chromosome
B. Plasmids
C. Ribosomes
D. Internal Membranes
E. Endospores
F. Reserve Materials
G. Gas Vesicles
H. Carboxysomes
I. Heterocysts

II. EUKARYOTIC CELLS

A. Nucleus
B. Ribosomes
C. Mitochondria
D. Chloroplasts
E. Endoplasmic Reticulum
F. Golgi Apparatus
G. Microbodies
H. Vacuoles
I. Cytoskeleton
J. Reserve Materials

 

I. CAPSULE and SLIME LAYERS

II. PILI

III. FLAGELLA and CILIA

A. Structure

1. Prokaryotic cells
2. Eukaryotic cells

B. Cell Motility

 

I. NORMAL MICROBIOTA

A. Skin Habitat
B. Oral Microbiota
C. Gastrointestinal Zone
D. Respiratory Microbiota
E. Gentiourinary Microbiota

II. MICROBIAL TOXINS

A. Definitions

1. invasiveness
2. toxigenicity

B. Lipopolysaccharide
C. Protein Toxins

1. neurotoxins
2. enterotoxins
3. cytotoxins
4. virulent enzymes

 

I. BACTERIAL REPRODUCTION AND GROWTH

A. Reproduction (asexual)

1. binary fission
2. budding
3. sporulation

B. Kinetics of Bacterial Growth

1. Exponential growth from binary fission
2. Normal growth

 

I. INTRODUCTION

A. Heterotrophy vs. Autotrophy
B. Oxidation-Reduction Reactions
C. Energy Needs of Cells

II. TYPES OF HETEROTROPHY

A. Respiration
B. Fermentation (anaerobic)

III. AEROBIC RESPIRATION

A. Three Phases Involved
B. Glycolysis
C. Krebs Cycle (citric acid cycle, tricarboxylic acid cycle)
D. Oxidative Phosphorylation
E. Net Energy Production

IV. FERMENTATION

A. Glycolysis
B. Fermentation Reactions
C. Types of Fermentation

 

I. FOOD PRODUCTION

A. Food Spoilage

1. fruits and vegetable
2. meats

B. Food Preservation
C. Food Production

1. dairy products
2. bread
3. alcoholic beverages

II. FERMENTATION INDUSTRY

A. Pharmaceuticals
B. Organic Acids
C. Amino Acids
D. Enzymes
E. Solvents
F. Synthetic Fuels
G. Vitamins
H. Polysaccharides
I. Enhanced Recovery of Mineral Resources

1. bioleaching
2. tertiary oil recovery

 

I. TYPES OF AUTOTROPHY

A. Autotrophic Cells
B. Photoautotrophy
C. Chemoautotrophy

II. PHOTOAUTOTROPHY

A. ATP formation and proton and/or electron transport
B. During photosynthesis, however, . . .
C. Photosynthesis consists of light-dependent and light-indepedent (i.e.. dark) reactions
D. Photosynthetic Pigments

1. Overview
2. Different Photosynthetic Organisms Contain Different Pigment Compositions
3. Structure and function of chlorophylls
4. Structure and Function of Carotenoids
5. Structure and Function of Phycobilins

E. Light-Dependent Reactions

1. Relation of Light and Dark Reactions
2. Reaction Centers are photosynthetic pigments organized into photosynthetic units in membranes
3. Anaerobic Photosynthesis - Photosystem I
4. Aerobic Photosynthesis - Photosystems I and II

F. Dark (Light-independent) Reactions

1. Green sulfur bacteria use a reversal of the tricarboxylic acid cycle and glycolysis to synthesize carbohydrates.
2. Calvin Cycle (C3 pathway)

III. CHEMOAUTOTROPHY

A. Chemoautotrophic (or chemolithotrophic) activities form critical links in the biogeochemical cycles of S, Fe, N, and C

B. Aerobic Chemoautotrophy

1. Types of organisms - Eubacteria
2. Types of reactions
3. Energetics of reactions (electron transport phosphorylation)

C. Anaerobic Chemoautotrophy

1. Types of organisms - Eubacteria and Archaebacteria
2. Types of reactions
3. Energetics of reactions - more ATP produced per NADH produced because H₂ has more reducing power
4. Methanogenic organisms are extremely sensitive to oxygen and oxidized compounds

 

MICROBIAL ECOLOGY

I. INTRODUCTION

II. BIOGEOCHEMICAL CYCLING

A. Concept of Trophic Levels
B. Central Role of Microorganisms in Carbon Cycling
C. Unbalanced Carbon Cycles - Sewage Disposal
D. Role of Microorganisms in the Inter-relationship of Elemental Cycles

III. UNUSUAL MICROBIAL HABITATS

A. Subterranean Microbial Communities
B. Endolithic Microbial Communities
C. Hydrothermal Vent Communities

IV. MICROBIAL BIOFILMS

A. Structure
B. Oxygen Demand in Biofilms

1. demand for oxygen exceeds diffusion of oxygen into biofilms
2. anaerobic conditions can develop within a 0.25 mm in the film
3. the same forms of anaerobic respiration seen in deeper sediments can develop in biofilms

C. Examples

1. Dental plaque
2. Trickling filters
3. Films on metal surfaces

D. Role of Biofilm Communities in Metal Corrosion

1. Biofilm bacteria do not attack metal directly
2. Anaerobic sulfate-reducing bacteria produce H₂S that complexes with iron ions from metal establishing an anode (net "-" charge) in the unaerated film
3. Sulfate-reducing activity thus establishes an electrochemical gradient leading to the loss of metal due to electrolysis. Hard to stop after it starts.

V. BACTERIA AND POLLUTION

A. Biodeterioration

1. Several billion $ are lost each year to biodeterioration
2. Microbial mineralization is responsible for most of the CO2 that is reinjected into the atmosphere
3. Effect on paper production

B. Biological Treatment of Wastes
C. Mercury

1. Sources
2. Sinks
3. Processes important in mercury biotoxicity and biomagnification

D. Polychlorinated Biphenyls and Dioxins

1. Structure
2. Toxicity
3. Sources
4. Biodegradation
   

I. OVERVIEW

A. Amphibolic pathways - dual purpose pathways
B. Pathways involving carbohydrates, lipids, proteins, and nucleic acids are all interconnected; they are not separate, isolated paths.

 

I. REVIEW

A. DNA Structure
B. Terms

II. REPLICATION

A. DNA replication is semiconservative in both prokaryotes and eukaryotes
B. Mechanics of Replication

1. Origin of replication - single origin usually internal (300 base sequence)
2. Replication fork
3. Leading strand
4. Lagging strand
5. Regulation of replication

III. TRANSCRIPTION (mRNA synthesis)

A. Differences compared to DNA
B. Mechanics of mRNA synthesis

1. RNA polymerase
2. DNA acts as template
3. Sigma subunit of RNA polymerase recognizes the appropriate site on DNA for the start of mRNA synthesis
4. RNA polymerase (sigma subunit) binds at a promoter region and opens up DNA helix
5. Only one strand of DNA is transcribed at a time
6. Moving RNA polymerase unwinds DNA, transcribes, and DNA rewinds
7. First base of mRNA is almost always A or G
8. Synthesis proceeds from 5' phosphate to 3'-OH
9. Sigma subunit of RNA polymerase is release after a few bases have been transcribed
10. mRNA synthesis is stopped when RNA polymerase reaches a termination sequence on DNA template

C. Differences between prokaryote and eukaryote mRNAs

1. Prokaryotes mRNA
2. Eukaryotic mRNA

IV. TRANSLATION (protein construction)

A. Three Types of RNA Involved

1. mRNA - already discussed
2. tRNA
3. Ribosomal RNA (rRNA)

B. Genetic Code

1. Triplet code (64 possible codes)
2. Redundance of triplet code (codes for 21 amino acids found in proteins)
3. Nonsense codes
4. Wobble concept - base pairing is less critical for the third base in a codon
5. Area between start and stop codes is an open reading frame. This is equivalent to the term gene.
6. Translation error is a big source of mutations

C. Mechanics of Protein Synthesis

1. Eukaryotes - mRNA moves through nuclear membrane pores and enters cytoplasm where translation takes place
2. Energy for protein synthesis comes GTP
3. Steps in protein synthesis

V. REGULATION OF PROTEIN SYNTHESIS

A. Negative Control - RNA polymerase function normally blocked

1. Induction - an inducer molecule removes a repressor molecule from blocking RNA polymerase to transcribe DNA Example - lac operon in E. coli
2. Repression - a repressor molecule will attach to DNA in the presence of a corepressor molecule. This prevents RNA polymerase from transcribing open reading frames on DNA Example: trp operon (co-repressor)

B. Positive Control

1. Regulator protein promotes the binding of RNA polymerase increasing mRNA synthesis - RNA polymerase function normally not blocked
2. Catabolite repression

C. Attenuation - regulation of transcription by translation in prokaryotes

1. Leader sequence - when transcribed prevents further transcription of structural genes
2. Example: trp operon

D. Differences in Regulation Between Prokaryotes and Eukaryotes

VI. MUTATION

A. Point Mutations

1. Base substitutions - occur during DNA replication
2. Frame-shift mutations
3. Reversions
4. Suppressor mutations - correction to wild type by restoring function at another site

B. Transposition Mutations - movement of information (genes) between different DNA molecules (a reshuffling of genes)

1. Insertion sequences
2. Recombination

C. Rates of Mutation

1. Point mutations - 10^-5/generation
2. Transpositions - 10^-4/generation

D. Factors Affecting Mutation Rate

1. Physical factors
2. Chemical factors

VII. TRANSFER OF DNA - RECOMBINATION

A. Prokaryotes

1. Transformation
2. Transduction
3. Conjugation

B. Eukaryotes

1. Alternation of generations between diploid and haploid stages
2. Meiosis
3. Cytoplasmic inheritance

VIII. GENETIC ENGINEERING

A. Terms
B. Steps in gene cloning
C. Principles at the basis of genetic engineering
D. Practical Applications
E. End product of genetic engineering is different from natural genetic mechanisms

 

I. EVOLUTION OF LIFE ON EARTH

A. Age of Earth - 4.6 BYBP
B. Earliest Fossil Microorganisms - Heterotrophy
C. Origin and Eubacteria and Archaebacteria
D. Origin of Photoautotrophy
E. Origin of Eukaryotic Cells - Symbiotic Theory

II. MOLECULAR APPROACH TO MICROBIAL PHYLOGENY

A. Microbial Species - has been considered as a group of isolated strains that have an overall similarity and are different from other fundamental groups (not necessarily reproductively-isolated like higher plants and animals)
B. rRNA's as the Ultimate Molecular Chronometers
C. Analysis of Sequence Alignments Revealing Microbial Relatedness
D. Universal Phylogenetic Tree
E. Eubacterial Phylogeny
F. Archaebacterial Phylogeny
G. Eukaryotic Phylogeny

 

I. BACTERIAL TAXONOMY - Bergey's Manual of Determinative Bacteriology

A. Characteristics for Classifying Bacteria
B. Groups in Bergey's Manual (19 groups)

II. FUNGAL TAXONOMY

III. ALGAL TAXONOMY

IV. PROTOZOAN TAXONOMY

I. STRUCTURE OF VIRUSES

A. Terms
B. Basic Viral Forms
C. Envelopes

II. CLASSIFICATION OF VIRUSES

A. Primary Characteristics
B. Secondary Characteristics

III. DIFFERENCES BETWEEN VIRAL PATHOGENS

A. Bacteriophages
B. Plant Viruses
C. Viruses of Vertebrates

IV. GROWTH AND REPRODUCTION OF VIRUSES

A. Conditions Necessary for Reproduction
B. Types of Reproduction
C. Growth Cycle (One-Step Growth Curve)

V. ASSAY OF BACTERIOPHAGES

A. Scanning Electron Microscopy
B. Phage Plaques

 

I. PHYSICAL CONTROL AGENTS

A. Temperature
B. Oxygen
C. Water
D. Pressure
E. pH
F. Radiation

II. CHEMICAL CONTROL AGENTS

A. Nutrition
B. Inhibitory chemicals - concentration and contact time determines effectiveness

III. ANTIBIOTICS

I. IMMUNE SYSTEM

II. HOST DEFENSE MECHANISMS

A. Outer Barriers
B. Phagocytosis
C. Interferons
D. Inflamatory Response

III. ACQUIRED IMMUNITY

A. Antibody Mediated Response

1. Terms
2. Classes of antibodies
3. Synthesis of antibodies
4. Culture of hybridomonas
5. Antigen-Antibody reactions

B. Cell Mediated Response

1. Eliminating infections within host cells
2. Two types of T-cells involved
3. Lymphokines
4. Complement system

IV. IMMUNITY DYSFUNCTION

A. Immunodeficiency
B. Hypersensitivity
C. Problems During Transplantations
D. Autoimmunity

V. HUMAN DISEASES

A. Respiratory Tract
B. Gastrointestinal Tract
C. Gentio-Urinary Tracts
D. Entering Through Skin
E. Direct Contact Diseases
F. Would Infections
G. Eye Infections
H. Oral Infections

 

 

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