Lecture #1 V2 - Introduction & Molecular Bondng

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Biology 301 Cellular and Molecular Biology Fall 2002

Lecture # 1: Introduction & Molecular Bonding

Course Organization This course covers the biological principles relating to cellular and subcellular levels of organization. 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: TBD Office phone: TBD Email: [email protected] Lectures: Tuesday & Thursday Discussion: Tuesday Laboratory: Thursday

Office Hours: TBD 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.

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Objectives of the course

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

1.

Understand the basics of molecular bonding and the special role of water in biochemical reactions

2.

Describe the structure of carbohydrates, lipids, nucleic acids and proteins

3.

Describe how enzymes function

4.

Describe how prokaryotic and eukaryotic cells regulate gene expression

5.

Identify the components of prokaryotic and eukaryotic cells and their respective functions

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 descriptive report of the results

Course Policies

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

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: A: 100-90%, B: 89-80%, C: 79-70%, D: 69-60%, F: 59% and below 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 discussion section is highly suggested since we will be actively discussing problems and articles. Attendance for laboratory is mandatory. 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. Dr. Gurel should be notified as soon as possible that you will be 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.

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Course Syllabus Text chapter assignments 2,4

3/18 – 3/22

Water & pH

3

3/25

Transport Channels

8

1/30

Carbohydrates & Lipids

5

3/27

Cell Signaling & Signal Transduction

11

2/4

Proteins

5

3/29

LAST DAY TO WITHDRAW

2/6

Enzymes

6

4/1

Cell Architecture

2/11

Nucleic Acids

5

4/3

Cytoskeleton & Cell Junctions

7

Mitosis & Cell cycle regulation

12 13

Date 1/23

Lecture Topics Introduction / Molecular Bonding

1/28

Lecture Topics

Date

Text chapter assignments

Spring Break

2/13

DNA Replication

16

4/8

2/18

Gene Expression I

17

4/10

Meiosis EXAM II (covers lectures 2/25 through 4/3)

7

2/20

Gene Expression II

17

4/15

2/25

Prokaryotic Gene Expression I

18

4/17

Energy / ATP / Oxidation & Reduction

18

4/22

Glycolysis & Fermentation

9

6, 9

2/27

Prokaryotic Gene Expression II

3/4

EXAM I (covers lectures 1/23 through 2/20)

4/24

The Krebs (Tri-carboxylic acid) cycle

9

3/6

Eukaryotic Gene Expression I

19

4/29

Electron Transport & Chemiosmosis

9

3/11

Eurkaryotic Gene Expression II

19

5/6

Photosynthesis I

10

3/13

Plasma Membrane Structure

8

5/8

FINAL EXAM

Laboratory Policies

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

(I) No eating, drinking or smoking is allowed in the laboratory. (2) You should arrive on time and be prepared to stay for the entire three hours. (3) Come prepared for the laboratory. Read the Introduction and procedures before coming to lab. Turn in your answers to the pre-lab questions at the beginning of lab. Late answers will not be accepted. (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 5 points will be deducted for each class period met after the due date. (5) While I encourage students 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.

Laboratory Syllabus Lab #

Date

01 & (W1)

1/23

Introduction to the Laboratory

02

1/30

Introduction to Spectrophotometry

03

2/6

Assay for Proteins

04

2/13

Enzymes Kinetics

W4

2/20

Restriction Digestion

W5

2/25 (Mon)

Isolation of Genomic DNA from Vibrio fischeri (Part I)

W5

2/27

Isolation of Genomic DNA from Vibrio fischeri (Part II)

W7

3/6

Spectrophotometric Analysis of DNA

W8

3/11 (Mon) & 3/13

Restriction Digestion of Genomic DNA & Plasmid Vector

W10

3/27 & 4/3

Ligation of Restriction Fragments of Genomic DNA to Plasmid Vector

W11 W12

4/10

Preparation of competent E. coli DH5α & Transfromation of competent E. coli with recombinant plasmids (Part I)

W12

4/17

Plate Genomic Library (Part II)

W13

4/24

Screening of the Genomic Library for light producing clones

13

5/1

Membrane Permeability

Experiment

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Lecture One: Overall outline Themes of biological structure & function Molecular Bonding Carbon … the central atom of life Moving beyond carbon

Themes of biological structure & function Hierarchical structure & function Emergent properties The cell is the fundamental biological unit Genetic inheritance Correlation of structure & function Regulatory mechanisms Evolution: Diversity & unity

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Molecular bonding Atomic constituents of life Electronic structure of atoms Electronic structures of elements in the first three rows of the periodic table Covalent bonding Polar covalent bonding Molecular geometry: VSEPR theory Ionic bonding Weak chemical bonds: Hydrogen bonding Neurochemical communication Molecular mimicry: the endorphins & morphine

Atomic constituents of life

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Electronic structure of atoms

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

First three rows of the periodic table: electronic structures

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Covalent bonding

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Polar covalent bonding

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Molecular geometry: VSEPR theory

Ionic bonding

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Weak chemical bonds: Hydrogen bonding

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Neurochemical communication

Molecular mimicry: the endorphins & morphine

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Carbon … the central atom of life Some simple carbon-based molecules Variations in carbon skeletons Hydrocarbons & soaps Three types of isomers Structural isomers: butane & isobutane Pharmacological importance of enantiomers

Some simple carbon-based molecules

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Variations in carbon skeletons

Hydrocarbons & soaps

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Three types of isomers

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Structural isomers: butane & isobutane

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Pharmacological importance of enantiomers

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Moving beyond carbon … Valences of H, O, N & C A comparison of functional groups in estrone and testosterone Molecular models of estrone and testosterone Functional groups of organic compounds Functional groups continued A model of a protein molecule … but arguably the most important molecule is simple water!

Valences of H, O, N & C

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

A comparison of functional groups in estrone and testosterone

Molecular models of estrone and testosterone

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Functional groups of organic compounds

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Functional groups continued

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

A model of a protein molecule

Ogan Gurel, MD Biology 301 Lecture #1 Roosevelt University

… but arguably the most important molecule is simple water!