Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
402023042006PROKARYOTIC DIVERSITY-ICompulsory357
Level of Course Unit
First Cycle
Objectives of the Course
Even a superficial examination of the microbial world shows that prokaryotes are the one of the most important groups. Much of our understanding of phenomena in ecology, biochemistry and molecular biology comes from research on prokaryotes. Therefore, microbial morphology and cell structure is very important subject. It is known, there are two quite different groups of prokaryotes: Domain Bacteria and Domain Archaea. The goal of this course is to explain what prokaryotic diversity and how this scientific discipline can realistically impact on our life.
Name of Lecturer(s)
Prof. Dr. Füsun B. UÇAR
Learning Outcomes
1To recognize the general data on microbial phylogeny and three domains of life by using methods of conventional and molecular biology
2To gain skills to adapt the data obtained about the general structures of prokaryotic cells to everyday life
3To gain skills in order to synthesize the energy mechanisms and physiology of prokaryotic cells by establishing a relationship between their life cycles and pathogenity in the nature
4To gain skills in order to recognize and interpret the effects of antibiotics produced by bacteria on human, plant and animal diseases
5To gain skills in order to recognize basic factors in the development of resistance mechanism of prokaryotic cells to antibiotics and to establish a relationship between these factors and the evolutionary process, and to struggle with them
6To improve the capacity to investigate the database about prokaryotic cells and to interpret these data
7To gain skills in order to establish a relationship between phenotype and genotype of prokaryotic cells and to apply all these data in every aspect of life
Mode of Delivery
Face to Face
Prerequisites and co-requisities
None
Recommended Optional Programme Components
None
Course Contents
Microbial phylogeny, three domains of life; phenotypic and genotypic identification of prokaryotic cells; microbial systematic; phylogenetic analysis; genomik fingerprint, aminoacid sequencing methods, molecular chronometer, phylogenetic trees; Species concept, classification phylum used of identification according to “Bergey’s Manuel of Systematic Bacteriology“; Prokaryotic (Bacteria and Archaea) cell morphology, cell wall structure; cell wall synthesis and the mechanism of antibiotics action to wall synthesis, structure and function of Penisilin binding proteins (PBP), Function and role of periplasm in gram negative bacteria; Cytoplasmic membrane structure and function, transport proteins and transport types (active transport and group translocation) and Protein export and protein secretion types; structure and synthesis of flagel, the physiology of flagellar motility, different motility types, archaeal flagel structure; Chemotaxi and other taxi types, Adaptation mechanism; Structure of bacterial endospore, genetic mechanism of endospore synthesis; bacterial differentiation types; Endospore germination, stage of outgrowth; Cell surface structures and inclusions; Gas vesicules; controls of prokaryotic cells; the effect of antibiotics to prokaryotic cell wall, cell membrane, RNA and DNA; integron, gene cassettes, super integrons, horizontal gene transfer
Weekly Detailed Course Contents
WeekTheoreticalPracticeLaboratory
1Microbial phylogeny, three domains of life; phenotypic and genotypic identification of prokaryotic cells; microbial systematicPrinciples of microscopes, simple staining of microorganisms
2Phylogenetic analysis; genomik fingerprint, aminoacid sequencing methods, molecular chronometer, phylogenetic treesNegative staining of microorganisms, measurement of cell size
3Species concept, classification phylum used of identification according to “Bergey’s Manuel of Systematic Bacteriology“; Prokaryotic (Bacteria and Archaea)Gram-staining method
4Cell wall structure; cell wall synthesis and the mechanism of antibiotics action to wall synthesis, structure and function of Penisilin binding proteins (PBP)Acid-fast staining method
5Function and role of periplasm in gram negative bacteriaEndospore staining method
6Cytoplasmic membrane structure and function (Bacteria and Archaea)Capsule staining method
7Transport proteins and transport types (active transport and group translocation); Protein export and protein secretion typesFlagella staining method
8Midterm ExamPHB, metacromatic granule and cell wall staining
9Structure and synthesis of flagel, the physiology of flagellar motility, different motility types, archaeal flagel structureMidterm exam
10Chemotaxi and other taxi types, Adaptation mechanism Nutritions requirements of microorganisms, types of media, preparation of media
11Structure of bacterial endospore, genetic mechanism of endospore synthesis; bacterial differentiation types; Endospore germination, stage of outgrowthMethods of obtain pure cultures
12Cell surface structures and inclusions; Gas vesiculesCultural characteristics of microorganisms
13Controls of prokaryotic cellsPhysical and chemical control of microorganisms
14The effect of antibiotics to prokaryotic cell wall, cell membrane, RNA and DNA integron, gene cassettes, super integrons, horizontal gene transferAntibiogram of microorganisms
15Mechanism of resistance to antibotics of prokaryotic cellsFinal exam
16Final Exam
Recommended or Required Reading
•Willey, J.M., Sherwood, L.M. and Woolverton, C.J. Prescott, Harley, and Klein’s Microbiology, 7th Ed, Mc Graw Hill Higher Education, 2008. •Madigan, M.T., Martinko, J.M., Dunlap, P.V. and Clark, D. P., Biology of Microorganisms 12th Ed, Pearson. USA. 2009. •Kim, B.H. and Gadd, G.M., Bacterial Physiology and Metabolism,1th Ed, Cambridge University Press, 2008.
Planned Learning Activities and Teaching Methods
Activities are given in detail in the section of "Assessment Methods and Criteria" and "Workload Calculation"
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
Midterm Examination175
Laboratory Examination125
SUM100
End Of Term (or Year) Learning ActivitiesQuantityWeight
Final Examination1100
SUM100
Term (or Year) Learning Activities40
End Of Term (or Year) Learning Activities60
SUM100
Language of Instruction
Turkish
Work Placement(s)
None
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination166
Final Examination166
Report Preparation6318
Report Presentation9545
Criticising Paper12672
Self Study4312
Individual Study for Mid term Examination166
Individual Study for Final Examination166
Reading14228
TOTAL WORKLOAD (hours)199
Contribution of Learning Outcomes to Programme Outcomes
PO
1
PO
2
PO
3
PO
4
PO
5
PO
6
PO
7
PO
8
PO
9
PO
10
PO
11
PO
12
PO
13
PO
14
LO154      4    5
LO25           4 
LO3 5    5  4  45
LO45       4  5  
LO5  5      5  5 
LO65  4    5  5 5
LO75   4        5
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
 
Ege University, Bornova - İzmir / TURKEY • Phone: +90 232 311 10 10 • e-mail: intrec@mail.ege.edu.tr