Syllabus V9 - Fall 2002 - Cell & Molecular Biology
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Biology 301 Cellular and Molecular Biology Fall 2002
This course covers the biological principles relating to cellular and subcellular levels of structure and function. Topics include introductory biochemistry and molecular biology as well as the fundamentals of cell structure and physiology. Implications of these basic principles for medical science will be considered as appropriate. Lecturer: Dr. Ogan Gurel Office Hours: After class Email: [email protected] Lectures: Tuesdays & Thursdays Discussion: Tuesdays Laboratory: Thursdays
6:00 - 7:15 PM 7:20 - 8:20 PM 7:30 - 9:50 PM
Prerequisites: Biology 150, Chemistry 202 and Chemistry 211 Texts
Required: Text: Campbell, Reece and Mitchell, (2002), Biology 6th ed. Benjamin/Cummings Lab: Winfrey, Rott and Wortmann, (1997), Unraveling DNA, molecular biology for the laboratory. Prentice Hall. Suggested: Martha A. Taylor, (2002), Student study guide for Cambell's Biology 6th edition. Benjamin/Cummings.
Objectives: This is a survey course in cellular structure and function. Upon completion you should be able to: 1. Understand the fundamentals of molecular bonding and the special role of water 2. Describe the structure of carbohydrates, lipids, nucleic acids and proteins 3. Describe how enzymes function 4. Identify the components of prokaryotic and eukaryotic cells and their respective functions 5. Describe how prokaryotic and eukaryotic cells regulate gene expression 6. Understand basic cell membrane structure and function 7. Describe the phases and events in the cell cycle 8. Understand basic cell metabolism – in particular, the biochemical pathways involved in the production of energy 9. Conduct basic experiments and write a intepretative report of the results
COURSE PROCEDURES & POLICIES Course Grades: Grades will be based on 1. Three 100 point exams 2. Laboratory exercises (150 points total) Exams consist of a mix of multiple choice, matching, true/false, short answer, and problems Grading Scale: Based on a class specific curve
Attendance policy: While attendance for lectures is not required, it is highly suggested. Borderline grades will be decided based on attendance, individual effort and class participation. Attendance for the discussion section is highly recommended since we will be actively discussing problems and articles. Attendance for laboratory, on the other hand, is mandatory. It is difficult, if not impossible, to understand how and why a technique works if you do not actually perform the experiment in the lab. In addition, many of the lab session build upon experiments conducted in the previous session. As such, it will be impossible to continue the remaining experiments. In the case that you must miss a lab due to personal or family illness, funerals, or religious or work- related commitments, the instructor should be notified prior to the lab so that alternate arrangements can be made. If you miss more than two laboratories, you must repeat the entire laboratory section. Missed Exams: Only doctor's orders, family illness or death in the family and acts of God are considered excusable reasons for missing an exam. Proper documentation is required. The instructor should be notified as soon as possible if you are unable to take an exam. Make up exams will be oral. Dishonesty: Dishonesty of any kind including cheating or plagiarism will not be tolerated. All matters of dishonesty will result in failure for the course. Plagiarism includes submitting another student's work as your own, presenting information from others' work as your own, and presenting information, even from the text or the laboratory manual, without recognition of the source. Work done in collaboration with others and attributed appropriately is permissible but must be discussed with the instructor beforehand.
LECTURE SCHEDULE (revised) TEXT CHAPTER
DATE 9/5
LECTURE TOPICS Introduction / Molecular Bonding
9/10
Water & pH
3
9/12
Carbohydrates & Lipids
5
9/17
Proteins (no lecture on 9/19 – lab only)
5
9/24
Enzymes
6
9/26
Nucleic Acids
5
10/1
DNA Replication
16
10/3
Gene Expression I
17
10/8
Gene Expression II
17
10/10
Prokaryotic Gene Expression I
18
10/15
Prokaryotic Gene Expression II
18
10/17
EXAM I (covers lectures 9/5 through 10/8)
10/22
Eukaryotic Gene Expression I
19
10/24
Eukaryotic Gene Expression II
19
10/29
Biology of Cancer
19
10/31
Plasma Membrane Structure, Transport Channel, Cell Signaling & Signal Transduction
11/7
No Lecture (Lab starts at 6pm)
NA
11/12
Cell Architecture: Cytoskeleton & Cell Junctions
11
11/14
No Lecture (Lab starts at 6pm)
NA
11/19
Mitosis, Cell Cycle Regulation, Meiosis and Recombination
11/21
EXAM II (covers lectures 10/10 through 11/12)
13
11/26
Energy / ATP / Oxidation & Reduction
6
12/3
Glycolysis & Fermentation
12/5
The Krebs Cycle
9
12/10
Electron Transport
9
12/12
Photosynthesis
10
12/17
FINAL EXAM (covers all the course material but emphasizes last third of lectures)
ASSIGNMENTS
2,4
19, 8
7, 12
6, 9
LABORATORY SCHEDULE: Lab Assistant: KatieLab manager: Binh [email protected] (847) 619-8582
General rules for the laboratory: 1. 2. 3.
No eating, drinking or smoking is allowed in the laboratory. You should arrive on time and be prepared to stay for the entire three hours. Come prepared for the laboratory. Read any relevant introductory materials and procedures before coming to lab. Please be ready to discuss the pre-lab questions at the beginning of lab. 4. Lab reports are due the week following an experiment unless otherwise stated. Each report is worth 10 points per week of experiments needed to complete the lab. Late reports will be accepted but depending on the circumstances, 5 points will be deducted for each class period met after the due date. 5. While students are encouraged to work together to solve problems both in class and in the laboratory, you must submit your own written reports. Follow the Guidelines for Laboratory Reports in the beginning of the laboratory manual when preparing your report. 6. Laboratory reports must be printed using a word processor or typed. No hand written reports will be accepted. Figures and graphs may be hand drawn. 7. The laboratory numbers correspond to the exercises in the laboratory handout given at the beginning of the semester. Exercises from the laboratory manual by Winfrey et al. are designated 'W4', 'W5' etc.
LAB #
DATE
EXPERIMENT
01 & (W1)
9/5
Introduction to the Laboratory
02
9/12
Introduction to Spectrophotometry
03
9/19
Bradford Assay for Proteins (lab only – no lecture)
04
9/26
Enzymes Kinetics
W4
10/3
Restriction Digestion
W5
10/10
Isolation of Genomic DNA from Vibrio fischeri (Part I)
W5
10/24
Isolation of Genomic DNA from Vibrio fischeri (Part II)
W7 & W8
10/31
Spectrophotometric Analysis of DNA; Restriction Digestion of Genomic DNA & Plasmid Vector (start)
W8 & W10
11/7
Restriction Digestion of Genomic DNA & Plasmid Vector; Ligation of Restriction Fragments of Genomic DNA to Plasmid Vector
W11 W12
11/14
Preparation of competent E. coli DH5α & Transformation of competent E. coli with recombinant plasmids (Part I)
W12
12/5
Plate Genomic Library (Part II)
W13
12/12
Screening of the Genomic Library for light producing clones
This course covers the biological principles relating to cellular and subcellular levels of structure and function. Topics include introductory biochemistry and molecular biology as well as the fundamentals of cell structure and physiology. Implications of these basic principles for medical science will be considered as appropriate. Lecturer: Dr. Ogan Gurel Office Hours: After class Email: [email protected] Lectures: Tuesdays & Thursdays Discussion: Tuesdays Laboratory: Thursdays
6:00 - 7:15 PM 7:20 - 8:20 PM 7:30 - 9:50 PM
Prerequisites: Biology 150, Chemistry 202 and Chemistry 211 Texts
Required: Text: Campbell, Reece and Mitchell, (2002), Biology 6th ed. Benjamin/Cummings Lab: Winfrey, Rott and Wortmann, (1997), Unraveling DNA, molecular biology for the laboratory. Prentice Hall. Suggested: Martha A. Taylor, (2002), Student study guide for Cambell's Biology 6th edition. Benjamin/Cummings.
Objectives: This is a survey course in cellular structure and function. Upon completion you should be able to: 1. Understand the fundamentals of molecular bonding and the special role of water 2. Describe the structure of carbohydrates, lipids, nucleic acids and proteins 3. Describe how enzymes function 4. Identify the components of prokaryotic and eukaryotic cells and their respective functions 5. Describe how prokaryotic and eukaryotic cells regulate gene expression 6. Understand basic cell membrane structure and function 7. Describe the phases and events in the cell cycle 8. Understand basic cell metabolism – in particular, the biochemical pathways involved in the production of energy 9. Conduct basic experiments and write a intepretative report of the results
COURSE PROCEDURES & POLICIES Course Grades: Grades will be based on 1. Three 100 point exams 2. Laboratory exercises (150 points total) Exams consist of a mix of multiple choice, matching, true/false, short answer, and problems Grading Scale: Based on a class specific curve
Attendance policy: While attendance for lectures is not required, it is highly suggested. Borderline grades will be decided based on attendance, individual effort and class participation. Attendance for the discussion section is highly recommended since we will be actively discussing problems and articles. Attendance for laboratory, on the other hand, is mandatory. It is difficult, if not impossible, to understand how and why a technique works if you do not actually perform the experiment in the lab. In addition, many of the lab session build upon experiments conducted in the previous session. As such, it will be impossible to continue the remaining experiments. In the case that you must miss a lab due to personal or family illness, funerals, or religious or work- related commitments, the instructor should be notified prior to the lab so that alternate arrangements can be made. If you miss more than two laboratories, you must repeat the entire laboratory section. Missed Exams: Only doctor's orders, family illness or death in the family and acts of God are considered excusable reasons for missing an exam. Proper documentation is required. The instructor should be notified as soon as possible if you are unable to take an exam. Make up exams will be oral. Dishonesty: Dishonesty of any kind including cheating or plagiarism will not be tolerated. All matters of dishonesty will result in failure for the course. Plagiarism includes submitting another student's work as your own, presenting information from others' work as your own, and presenting information, even from the text or the laboratory manual, without recognition of the source. Work done in collaboration with others and attributed appropriately is permissible but must be discussed with the instructor beforehand.
LECTURE SCHEDULE (revised) TEXT CHAPTER
DATE 9/5
LECTURE TOPICS Introduction / Molecular Bonding
9/10
Water & pH
3
9/12
Carbohydrates & Lipids
5
9/17
Proteins (no lecture on 9/19 – lab only)
5
9/24
Enzymes
6
9/26
Nucleic Acids
5
10/1
DNA Replication
16
10/3
Gene Expression I
17
10/8
Gene Expression II
17
10/10
Prokaryotic Gene Expression I
18
10/15
Prokaryotic Gene Expression II
18
10/17
EXAM I (covers lectures 9/5 through 10/8)
10/22
Eukaryotic Gene Expression I
19
10/24
Eukaryotic Gene Expression II
19
10/29
Biology of Cancer
19
10/31
Plasma Membrane Structure, Transport Channel, Cell Signaling & Signal Transduction
11/7
No Lecture (Lab starts at 6pm)
NA
11/12
Cell Architecture: Cytoskeleton & Cell Junctions
11
11/14
No Lecture (Lab starts at 6pm)
NA
11/19
Mitosis, Cell Cycle Regulation, Meiosis and Recombination
11/21
EXAM II (covers lectures 10/10 through 11/12)
13
11/26
Energy / ATP / Oxidation & Reduction
6
12/3
Glycolysis & Fermentation
12/5
The Krebs Cycle
9
12/10
Electron Transport
9
12/12
Photosynthesis
10
12/17
FINAL EXAM (covers all the course material but emphasizes last third of lectures)
ASSIGNMENTS
2,4
19, 8
7, 12
6, 9
LABORATORY SCHEDULE: Lab Assistant: KatieLab manager: Binh [email protected] (847) 619-8582
General rules for the laboratory: 1. 2. 3.
No eating, drinking or smoking is allowed in the laboratory. You should arrive on time and be prepared to stay for the entire three hours. Come prepared for the laboratory. Read any relevant introductory materials and procedures before coming to lab. Please be ready to discuss the pre-lab questions at the beginning of lab. 4. Lab reports are due the week following an experiment unless otherwise stated. Each report is worth 10 points per week of experiments needed to complete the lab. Late reports will be accepted but depending on the circumstances, 5 points will be deducted for each class period met after the due date. 5. While students are encouraged to work together to solve problems both in class and in the laboratory, you must submit your own written reports. Follow the Guidelines for Laboratory Reports in the beginning of the laboratory manual when preparing your report. 6. Laboratory reports must be printed using a word processor or typed. No hand written reports will be accepted. Figures and graphs may be hand drawn. 7. The laboratory numbers correspond to the exercises in the laboratory handout given at the beginning of the semester. Exercises from the laboratory manual by Winfrey et al. are designated 'W4', 'W5' etc.
LAB #
DATE
EXPERIMENT
01 & (W1)
9/5
Introduction to the Laboratory
02
9/12
Introduction to Spectrophotometry
03
9/19
Bradford Assay for Proteins (lab only – no lecture)
04
9/26
Enzymes Kinetics
W4
10/3
Restriction Digestion
W5
10/10
Isolation of Genomic DNA from Vibrio fischeri (Part I)
W5
10/24
Isolation of Genomic DNA from Vibrio fischeri (Part II)
W7 & W8
10/31
Spectrophotometric Analysis of DNA; Restriction Digestion of Genomic DNA & Plasmid Vector (start)
W8 & W10
11/7
Restriction Digestion of Genomic DNA & Plasmid Vector; Ligation of Restriction Fragments of Genomic DNA to Plasmid Vector
W11 W12
11/14
Preparation of competent E. coli DH5α & Transformation of competent E. coli with recombinant plasmids (Part I)
W12
12/5
Plate Genomic Library (Part II)
W13
12/12
Screening of the Genomic Library for light producing clones
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