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Of The City University of New York

Department Of Biological Sciences



SPRING 2003                                                                        Professor L. Brancaccio Taras

Course Description:  Bio 50, General Microbiology, is a one semester, 4 credit class with a lecture and laboratory (3 hours each).  The prerequisites for this course are one year of General Biology (Bio 13-14) and one semester of General Chemistry (Chm 11).   The diverse structure and activities of microbes in a wide number of environs will be examined.  Throughout the course, aspects of microbes beyond their ability to cause disease will be studied.  These include the use of microbes in food production, antibiotic production, and bioremediation.  Laboratory experiments will be conducted to support the concepts studied in the lecture portion of the course, the textbook readings, and other readings.  Basic microbiological techniques such as staining, aseptic transfer, and pure culture techniques will be conducted.  More advanced laboratories designed to demonstrate the interdisciplinary nature of microbiology will include collection of marine water and sediment samples for cultivation of algae and the isolation of antibiotic-producing microbes, and studies of various microbial relationships  using plants. 

Course Goals

 1.  Demonstrate an appreciation for the diverse microbial world with regard to the structure and function of microbes.

 2.  Perform basic microbiological techniques to stain, cultivate, and identify microbes.

 3.  Demonstrate the positive and negative effects microbes have on society resulting in historically  significant events.

 4.  Identify commensal, mutualistic, and antagonistic relationships microbes develop with other organisms.

 5.  Analyze the contributions microbes make to soil and aquatic environments by their roles in food webs and nutrient cycling.

 6.  Apply the interdisciplinary nature of microbiology to the fields of genetics, ecology, food production, and waste management.

TEXTBOOK Microbiology:  Essentials and Applications

 Larry McKane and Judy Kandel, 2nd ed. (1996) McGraw-Hill, Inc., New York

LAB MANUAL: Laboratory Exercises in Microbiology

                                    Loretta Brancaccio Taras and Joseph N. Muzio, 1st ed.(2002) Whittier Publications,

                                                Inc., New York

OTHER REQUIRMENTS:  A knee-length laboratory coat


Topical Outline


                        Significance of studying the field of microbiology

                        Survey of microbes studied:  bacteria, fungi, algae, protists, and viruses

                        Function of microbes in the environment and in basic research

                        Biogeochemical cycle                        

                        What would the world be like without microbes?          

                        History of microbiology:  From van Leewenhoek to the present

Text readings:  Chapter 1 p.  2-25;    Chapter 2   p.  27-45


                        Bacterial morphology (size, shapes and arrangements)

                        Bacterial structures  (cell membrane, cell wall, glycocalyx, cytoplasm, nucleoid, cytoplasmic

                                    inclusions, flagella, pili, and endospores)    

Text readings:  Chapter 4  p.  66-72;  74-96



                        Binary fission

                        Bacterial growth curve

                        Requirements for growth

                        Phototrophs, chemotrophs, autotrophs, and heterotrophs

                        Factors affecting microbial growth

                        Populations counts and determination of microbial numbers         

Text readings:  Chapter 5  p.  97-125

WEEK 3:            METABOLISM

                        Review of anabolism, catabolism, ATP, biomolecules, and enzymes

Text readings: Chapter 6  p.  126-149

                        Aerobic respiration, anaerobic respiration, types of fermentation, photosynthesis in

                                    eukaryotes and cyanobacteria

Text readings:  Chapter 7  p.  150-177


    &                Review of transcription and translation

WEEK 5:            Posttranslational processing in prokaryotes:  inteins and exteins

                        Regulation of gene expression:  induction, repression, operons, and attenuation


                        Genetic transfer in bacteria:  transformation, transduction, and conjugation

Text readings:  Chapter 8  p.  178-214

                        Gene cloning in bacteria

                        Transferring genes to animal cells:  gene replacement, antisense technology, and transgenic


Text readings:  Chapter 9  p.  215-236

WEEK 6:          FUNGI

                        Structures of fungi

                        Types of spores

                        Classification of fungi

                        Growth of fungi

                        Ecology of fungi

                        Association of fungi (mutualistic and parasitic)

Text readings:  Chapter 11  p.  225-279

WEEK 7:            PROTISTS

                        Structure of protists

                        Nutrition, metabolism and reproduction

                        Classification of protists

                        Classification and ecology of algae

                        Slime molds

Text readings:  Chapter 12  p.  280-304

WEEK 8:          VIRUSES

                        Viral structures



                        Oncogenic viruses

                        Viroids and prions

                        Viral cultivation

Text readings:  Chapter 13  p.  305-332


   &                 Commensalism

WEEK10:            Mutualism


Text readings:  Chapter 14  p.  333-346


    &                 Food webs

WEEK 11:            Nutrient cycling

                        Soil microbes

                        Aquatic microbes

                        Water treatment

                        Sewage disposal


Text readings:  Chapter 26  p.  704-734


   &                 Food production

WEEK 12:            Production of industrial and pharmaceutical products

                        Production of natural resources

                        Trends in microbiology and the future of microbiology

Text readings:  Chapter 27  p.  735-769


Sequence of Lab Experiments

Lab Manual:  Laboratory Exercises in Microbiology by L. Brancaccio Taras and J. N. Muzio

WEEK#                 EXERCISE TITLE                                                EXERCISE # (page)

     1                             Check In/ Safety rules                                                           

                                    Bright-field microscope  (review parts and                              1 (p.  3)

                                                Focusing procedure)             

                                    Smear preparation and simple staining                                    2 (p.  12)

                                    Negative Staining                                                                     3 (p.  20)                  

                                    Culture medium & aseptic transfer                                                10 (p.  57)

   2                               Gram staining                                                                                    4 (p.  25)

                                    Acid-fast staining                                                                  5  (p.  31)

                                    Capsule staining                                                                     6  (p.  36)

                                    Endospore staining                                                                  7  (p.  41)                  

                                    Pure culture techniques                                                       11 (p.  63)


   3                               Bacterial population counts                                                  12  (p.  70)

                                    Selective & differential media                                                  14  (p.  80)      

                                    Factors affecting microbial growth            

   4                               Water and sediment sampling                                                          27 (p.  181)                                                                                           

   5                               Isolation of antibiotic producers- Part I                           29 (p.  195)                

                                    Winogradsky column                                                             28 (p.  189)

                                    Determination of bacterial properties-

                                                Carbohydrate fermentation  Parts I-V                                  23 (p.  127)

                                    Determination of bacterial properties - 

                                                Protein metabolism            Parts I-III                                24 (p.  138)

   6                               Determination of bacterial properties - 

                                                Protein metabolism            Part IV- VI                          24 (p.  138)

                                    Determination of bacterial properties –

                                                Exoenzymes and endoenzymes Parts I-VII                   25 (p.  150)


  7                                Determination of bacterial properties-

                                                Identifying an unknown bacterium- Parts I & II            26 (p.  164)

                                    Analysis of the effectiveness of antiseptics and disinfectants            19 (p.  105)

                                    Kirby-Bauer method for analyzing the

                                                            effectiveness of antibiotics                                20  (p.  109)

                                    Analysis of the effectiveness of ultraviolet light             21 (p.  115)    


 WEEK#                EXERCISE TITLE                                                EXERCISE # (page)

     8                             Examination of molds                                                        32 (p.  223)                

                                    Examination of algae                                                          33 (p.  231)                

                                    Algal blooms                                                                       

     9                             Bioremediation                                                                    31 (p. 209)    
Protozoa and slime molds                                                  34 (p.  239)                                                                

   10                             Viruses                                                                                   35 (p.  249)                

                                    Water analysis                                                                        30 (p. 205)   
Commensalism                                                                      37 (p. 265)    

Mutualism- Parts I, II, and III                                                 38 (p.  269)

Antagonism- Parts I and II                                                            39 (p.  275)           

   11                     Bacterial genetic transfer-transformation                                                                                                
Food microbiology- Bacterial counts of food samples         42 (p.  301)    

                                    Use of chemical preservatives to increase the shelf

                                                life of apple cider                                                       43 (p.  305)

                                    Analysis of the effectiveness of hand washing                  22 (p.  119)                                                                                                      

  12                              Analysis of results from week 11


BIO 50


The objectives listed can be used as guidelines for studying each topic considered in the course.

Introduction and History of Microbiology

 1.  Describe in several sentences the significance of the contributions of the following scientists to

            the field of microbiology:  (a) van Leewenhoek;  (b)  Pasteur;  (c)  Jenner; 

            (d)  Semmelweis;  (e)  Lister;  (f)Koch; (g) Ehrlich;  and (h) Fleming.

 2.  Define spontaneous generation.

 3.  In a brief statement, describe the series of experiments disproving spontaneous generation.

 4.  List 3 three ramifications resulting from the removal of all microbes from the earth.

 5.  List 5 beneficial activities of microbes in the environment.

 6.  List 3 beneficial activities of microbes that benefit humans.

 7.  List 3 detrimental activities of microbes.

 8.  Describe biogeochemical cycling.  Include the classes of organisms involved and their activity in this process.

 9.  Define germ theory.

10.  Describe Robert Koch’s experiment proving germ theory.

11.  List the 4 criteria of Koch’s postulates.

12.  List 3 identifying characteristics used to distinguish the following organisms studied in microbiology:  (a)  bacteria;  (b)  fungi;  (c)  protozoa;  (d)  algae;  and (e)  viruses.

13.  List 2 activities carried out by each of the microbes listed in objective #12.

Bacterial Structures and Shapes  

 1.  Define the term morphology. 

 2.  Draw and name the 3 most common bacterial shapes and their arrangements.

 3.  Define the term pleomorphic. 

 4.  Describe the chemical composition (structure) and function of the following bacterial organelles: (a)cell wall;  (b) cell membrane; (c) glycocalyx; (d)endospores; (e) flagella; 

            (f)  pili;  (g) inclusion bodies; (h)plasmid;   and  (i)  nucleoid.

 5.  State the chemical differences in the cell walls of Gram-positives, Gram-negatives, and archaebacteria.

 6.  Name the components of the outer membrane of a Gram-negative.

 7.  Explain the action of penicillin and lysozyme in relation to bacterial cell walls.

 8.  Draw and name the 4 bacterial flagellar arrangements.

 6.  Explain the difference between sporulation and germination.

 7.  Draw and name the 3 endospore locations within a cell.

Bacterial  Growth

 1.  Describe in a series of steps the process of binary fission.

 2.  Draw and label the four phases of a typical bacterial growth curve.

 3.  Describe the phases of a typical bacterial growth curve.

 4.  Define the term generation time.

 5.  Explain the function of a chemostat in maintaining a continuous culture.

 4.  Define the term fastidious microbes

 5.  Define each of the following terms with regard to their energy and carbon source: 

            (a) photoautotroph;(b) photoheterotroph;  (c) chemoautotroph;  and

            (d) chemoheterotroph. 

 6.  Describe how each of the following physical factors affect microbial growth:  (a) temperature;  (b) pH; (c) molecular oxygen;  (d) osmostic pressure.

 7.  Define the term culture medium.

 8.  Explain the difference between a chemically defined and a complex culture medium.

 9.  Explain the difference between a selective and a differential culture medium.

10.  Explain the difference between a direct and indirect method for measuring microbial growth. 

11.  Name 1 direct method for measuring microbial growth and describe how it is performed.

12.  List 1 advantage and 1 disadvantage of the method mentioned in objective #11.

13.  Name 2 indirect methods for measuring microbial growth and describe how each is performed.

14.  List 1 advantage and 1 disadvantage of the methods mentioned in objective #13.

15.  Define the term bioassay and explain how bioassays are used to measure microbial growth.


 1.  Define the following terms:  (a) metabolism; (b) catabolism; and (c) anabolism.

 2.  Define what an enzyme is and state how enzymes increase the rate of a biochemical reaction.

 3.  Name the 4 macromolecules found in all cells.

 4.  Write 4 chemical reactions demonstrate the anabolism of the 4 macromolecules mentioned in

objective #3.

 5.  Write 4 chemical reactions demonstrate the catabolism of the 4 macromolecules mentioned in

            objective #3.

6.  Define the following terms:  (a) fermentation; (b) aerobic respiration; and (c) anaerobic respiration.

 7.  List the end products of (a) glycolysis; (b) Krebs cycle;  (c)  electron transport/oxidative


 8.  Explain how carbohydrates, proteins, and lipids are metabolized to generate ATP.

 9.  Explain the significance of microbial metabolism in the identification of microorganisms.

10. Write a chemical reaction for each type of fermentation mentioned and name a microbe that carries out each type of fermentation:  (a) homolactic fermentation;  (b) mixed acid fermentation; and (c) alcoholic fermentation

11.  List three organisms and their fermentation products used in food production.

12.  Define the term photosynthesis and name a microbe of carrying out the reactions of photosynthesis.

13.  State 1 difference between photosynthesis of plants versus photosynthesis of microbes.

14.  Define the term chemoautotrophy (also known as chemolithotrophy).

Genetic Transfer

 1.  Define the following terms:  (a) gene; (b) genotype; (c) phenotype; and (d) mutation.

 2.  Distinguish between the processes of DNA replication, transcription and translation.

 3.  Explain RNA processing in prokaryotes.

 4.  Explain RNA processing in eukaryotes.

 5.  Define the term operon and describe the different genes and regulatory regions found in an operon.

 6.  Explain the difference between an inducible and a repressible operon with regard to the type of

            enzymatic pathway they are associated with, the effector, and the repressor protein.

 7.  Explain the process of catabolite repression using E.coli growing in broth with lactose and glucose.

 8.  Explain how each of the following causes mutations:  (a)base analogues, (b) ultraviolet light and

(c) transposable genetic elements.

 9.  Distinguish between transformation, transduction and conjugation. 

10.  Define the term competency.

11.  Explain the difference between specialized and generalized transduction.

12.  Explain the difference between a F+ cell, Hfr cell , and F’ cell.

13.  Explain how genetic transfer increases the ability of bacterial cells to survive under adverse conditions such as exposure to antibiotics or heavy metals.

14.  Explain the purpose of the Ames test and how it is performed.

15.  Briefly describe the 6 steps required to transfer a human gene to a bacterial cell for cloning purposes.

16.  List 2 advantages and 2 disadvantages of using human cloning products.

16.  Define the following terms:  (a) cDNA; (b) DNA library; (c) nucleic acid probe;

             (d) hybridization; 

17.  Name the bacterium commonly used to transfer genes to plants and explain the steps involved in creating recombinant plants.

18.  Define the following gene therapy techniques:  (a) gene replacement and

            (b) antisense technology.

19.  Define the following terms:  transgenic animals and “piggyback” vaccines.

20.  Explain the purpose of the polymerase chain reaction (PCR) procedure.


 1.  Define the term hyphae and explain the difference between septate and nonseptate hyphae.

 2.  Explain the difference between vegetative hyphae and aerial hyphae.

 3.  Name and describe the structure of the 4 types of sexual fungal spores.

 4.  Name and describe the structure of the 5 types of asexual fungal spores.

 5.  Name and describe the 5 taxonomic categories of fungi based on spore type (sexual and asexual) and  morphology of hyphae. 

 6.  Name 2 poison-producing fungi and the effects of these poisons.

 7.  State the conditions for optimal fungal growth with regard to temperature, pH, and glucose


 8.  List 1 example of the saprophytic activity of fungi in the environment. 

 9.  Describe the role of fungi in the following mutualistic relationships:  (a) lichen; (b) mycorrhizae

10.  List 2 examples to demonstrate the parasitic nature of fungi with humans and plants.


 1.  Explain the difference between protozoa and algae.

 2.  Distinguish between polymorphism and pleomorphism.

 3.  Name and define the 2 common life cycle forms of protozoa.

 4.  Name and describe the major mode of nutrient acquisition demonstrated by protozoa.

 5.  Explain the function of the contractile vacuole in protozoa.

 6.  Draw diagrams to demonstrate longitudinal binary fission, transverse binary fission, and multiple fission. 

 7.  Name and describe the 4 groups of protozoa. 

 8.  Name 2 pathogenic protozoa and the diseases they are responsible for.

 9.  Name 3 properties used to classify algae.

10.  Briefly explain the importance of algae in a marine food pyramid. 

11.  Describe how an algal bloom develops and its detrimental effects on a body of water.

12.  Draw a diagram to describe the life cycle of a plasmodial (acellular) slime mold.

13.  Draw a diagram to describe the life cycle of a cellular slime mold.


 1.  Explain why viruses are considered obligate intracellular parasites. 

 2.  Define the following parts of a virus:  (a) capsid; (b) capsomere; (c) nucleocapsid; (d) envelope; and (e) spikes.

 3.  List 5 properties used to classify viruses.

 4.  Name and describe the 5 steps involved for a virus to enter a host cell. 

 5.  Explain each of the following viral genetic material replication strategies:  (a) double-stranded DNA; (b) single stranded DNA; (c) positive strand RNA;  (d) negative strand RNA;  and (e)             retroviruses.

 6.  Draw a graph of a one-step growth curve, label the x and y axis, and the areas of the graph representing addition of virus to host cells, viral eclipse, and maturation.

 7.  Define the following terms:  (a) oncogenic virus; (b) viroid; and (c) prion.

Microbial Interactions

 1.  Define the following types of symbiosis:  (a) commensalisms; (b) mutualism; and (c) antagonism.

 2.  Distinguish parasitism from predation.

 3.  Explain how a lichen is an example of mutualism

 4.  Define the term endosymbiosis and give an example.

 5.  Define the term biofilm and give an example.

 6.  Name 2 examples of mutualism between:  (a) microbes and plants; and (b) microbes and animals.

 7.  Distinguish between antibiotics and bacteriocins.

Microbes in the Environment

 1.  Explain the energy and nutrient flow through a food web from producers to consumers.

 2.  Explain the carbon, nitrogen, sulfur and phosphorus are cycled.

 3.   Explain the following cycles including the microbes involved in the various reactions: 

            (a) carbon cycle; nitrogen cycle; (c) phosphorus cycle; and (d) sulfur cycle.

 4.  List 3 functions of microbes in soil.

 5.  List 3 functions of microbes in an aquatic environment.

 6. Explain the role of microbes in the following activities:  (a) corrosion; (b) eutrophication; and

(c) bioremediation.

 7.  Explain, in a series of steps, water treatment and sewage treatment and disposal.

Food and Industrial Microbiology

 1.  List 2 food products resulting from microbial fermentation and the name of the microbe.

 2.  List 5 microbial enzymes used in food production.

 3.  Explain 2 advantages and 2 disadvantages of genetically engineered food products.

 4.  Distinguish between a primary and secondary metabolite and give an example of each.

 5.  Give 2 examples of how microbes have been used to alter crops.

 6.  Describe the role of microbes in fuel production and mining.

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