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Chemistry 5N G
Organic and Biochemistry
(3 units lecture, 2 units lab)
TTh 4:15 – 5:30 pm A603
General Information
Text: General,
Organic, and Biochemistry, 4th ed. by Denniston, Topping, and Caret
References: Fundamentals of Organic Chemistry, 5th edition by John
McMurry
Biochemistry, 4th edition by Campbell & Farrell
Introduction to General, Organic and Biochemistry, 8th
edition by Bettelheim, Brown, Campbell & Farrell
Instructor:
Mr. Higinio R. Barros, Jr.
5th Floor, SC Building, Chemistry Department, Xavier University – Ateneo de Cagayan, Corrales Ave.,
Cagayan de Oro City
Email: gino_bschem@yahoo.com ; hrbarros@xu.edu.ph
Web page: http://ginobarros.tripod.com
Residence Hours: MWF 1:00 – 4:00 pm ; TTh 10:30 am – 12:00 nn
Course outline:
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Date |
Topics/Activity |
Readings (from textbook except where indicated otherwise) |
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Week 1 |
June 12 |
(No class) |
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June 14 |
Orientation
Introduction
to Organic Chemistry : Sources of Organic Compounds; Structure of Organic Compounds
Valence
Bond Theory |
pp. 294-297
pp. 387-390(Jones) |
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Week 2 |
June 19 |
Promotion &
Hybridization
Organic Functional
Groups
Alkanes: Structure;
Constitutional Isomerism; |
pp. 390-399(Jones)
pp. 298-300
pp. 300-303 |
|
|
June 21 |
Nomenclature
of Alkanes
Cycloakanes:
Shapes; Cis-Trans Isomerism
Physical Properties
of Alkanes; Reactions;
Important Haloalkanes
& Sources of Alkanes |
pp. 303-319 |
|
Week 3 |
June 26 |
Alkenes &
Alkynes: Structure; Cis-Trans Isomerism; Nomenclature including Cycloakene, Diene & polyene; Physical Properties; Naturally
occurring alkenes; Addition Reactions of Alkenes: Hydration; Hydrohalogenation, |
pp. 326-337
pp. 342-345 |
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June 28 |
Halogenation
& Hydrogenation; Polymerization of Ethylene;
Benzene: Structure;
Nomenclature & ReactionsPhenols: Structure & Nomenclature; Acidity; As Antioxidants; |
pp. 337-341
pp. 350-358 |
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Week 4 |
July 03 |
Exam on VBT, Hybridization, Alkanes & Alkenes & Alkynes
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July 05
(AVR 4) |
Alcohols: Nomenclature;
Classifications & Reactions: Ethers & Thiols: Properties & Reactions
Chirality:
Enantiomerism; R,S System |
pp. 364-387
pp. 396-406
(Organic & Biochem, 8th ed) |
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Week 5 |
July 10 |
Exam on Benzene & Alcohols, Ethers & Thiols
Molecules with
Two or More Stereocenters;Optical activity; Significance of Chirality in the
Biological world |
pp. 407-413
(Organic & Biochem, 8th ed) |
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July 12 |
Prelim Exam
Coverage: VBT, Hybridization |
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Week 6 |
July 17
(AVR 2) |
Amines: Structure;
Classification;Nomenclature;
Physical Properties;
Basicity; Reactions
Aldehydes &
Ketones: Structure; Nomenclature;Physical Properties; Oxidation & Reduction |
pp. 458-474
pp. 394-407 |
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July 19 |
(No class:
Faculty/Staff Recollection) |
|
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Week 7 |
July 24 |
Exam on Chirality & Amines
Addition of
Alcohols to Aldehydes & Ketones;
Keto-Enol Tautomerism
Carboxylic Acids: Nomenclature; Physical Properties |
pp. 410-413
pp. 422-429 |
|
|
July 26
(AVR 1) |
Acidity of
Carboxylic Acids & Reactions with Bases
Anhydrides,Esters
& Amides: Nomenclature
Preparation
of Esters & Amides
Hydrolysis
of Anhydrides, Esters & Amides
Phosphoric
Anhydrides & Esters
Step-Growth
Polymerizations |
pp. 430-450
pp. 475-478
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Week 8 |
July 31 |
(No class:
Feast of St. Ignatius) |
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Aug 02 |
Exam on Aldehydes, Ketones, Carboxylic Acids |
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Week 9 |
Aug
06-10 |
Midterm Week
Coverage for Midterm Exam: All Chapters in Organic Chemistry |
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Week 10 |
Aug 14 |
Carbohydrates:
Monosaccharides
Cyclic Structures
of Monosaccharides
Reactions of
Monosaccharides
Disacchariides;
Oligosaccharides &Polysaccharides |
pp. 490-517 |
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|
Aug 16
(AVR 3) |
Lipids: Classification,
Structure & Properties of Triglycerides; Complex Lipid; Membrane; Glycerophospholipid; Sphingolipid; Glycolipids
Steroids: Cholesterol;
Lipoproteins; Transport of Cholesterol; Steroid Hormones; Bile Salts; Prostaglandins; Thromboxanes & Leukotrienes |
pp. 522-556 |
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Week 11 |
Aug 21 |
(No class:
Ninoy Aquino Day) |
|
|
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Aug 23
(AVR 5) |
Proteins: Function;
Amino Acids; Zwitterions; Peptides & Proteins; Properties of Peptides & Proteins
Structure of
Proteins: Primary, Secondary, Tertiary & Quaternary; Glycoproteins; Denaturation of Proteins |
pp. 562-589 |
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Week 12 |
Aug 28 |
(No class:
City Fiesta) |
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Aug 30
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Exam on Carbohydrates & Lipids
Enzymes: Naming
& Classification; Factors Affecting Enzyme Activity; |
pp. 594-624 |
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Week 13 |
Sep 04
(AVR 2) |
Mechanism of
Enzyme Action
Enzyme Regulation;
Enzymes in Medical Diagnosis & Treatment
Reading Assignment:
Neutrotransmitters
& Hormones
Nucleotides,
Nucleic Acids & Heredity: Components; Structure of DNA RNA; Types of RNA Genes, Exons & Introns |
pp. 722-758 |
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Sep 06 |
Exam on Proteins & Enzymes
DNA Replication; DNA Repair; Cloning |
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Week 14 |
Sep 11
(AVR 2) |
Gene Expression
& Protein Synthesis: Transcription; The Genetic Code; Translation & Protein Synthesis; Gene Regulation Mutation, Mutagen
& Genetic Diseases; Recombinant DNA |
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Sep 13 |
Semi-final Exam |
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Week 15 |
Sep 18
(AVR 2)
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Bioenergetics:
Introduction; Principal Compounds of the Common Catabolic Pathway; Citric Acid Cycle Electron & H+ Transport;
Phosphorylation & Chemiosmotic Pump; Energy Yield; Conversion of Chemical Energy |
pp. 629-718 |
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Sep 20
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Exam on Gene Expression, Protein Synthesis & Bioenergetics |
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Week 16
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Sep 25
(AVR 3) |
Specific Catabolic
Pathways: Intro; Glycolysis; Pentose Phosphate Pathway; Energy Yield from Glucose; Glycerol Metabolism
ß-oxidation
of Fatty Acids; Energy Yield of Stearic Acid; |
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Sep 27
(AVR 5) |
Ketone Bodies;
Catabolism of Nitrogen and Carbon Skeleton of Amino Acids
Biosynthetic
Pathways: Intro; Biosynthesis of Carbohydrates, Fatty Acids, Lipids & Amino Acids |
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Week 17
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Oct 02
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Exam on Specific Catabolic Pathways & Biosynthetic Pathways
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Oct
03, 05
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Part of the
Final Week
Coverage for Final Exam: All Chapters in Biochemistry |
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*Changes in the schedule will be announced by the instructor.
Grading System
Lecture:
Midterm Grade = [PE + ME + (Chap Exams, Quizzes, Assignments,
etc.)] / 3
Final
Period Grade = [SFE + FE + (Chap Exams, Quizzes, Assignments, etc.)] / 3
Overall:
Midterm
Grade = (2/3)*Lec Grade + (1/3)*Lab Grade
Final
Period Grade = (2/3)*Lec Grade + (1/3)*Lab Grade
Final
Grade = (2/3)*Final Period Grade + (1/3)*Midterm Grade
Examinations: There are four major exams (Prelim, Midterm, Semifinal, and Final).
Quizzes and Assignments: Quizzes will be given depending on the need and will be usually announced. Questions
for quizzes are usually exercise questions / applications to practice the concepts learned but will sometimes be “objective”
type. They may be held before or after the lecture or activity, so students are held responsible to study and be prepared.
Assignments or homework/problem sets are given with the intention of encouraging self-study among students,
not just to review their lecture notes but also to pursue some skills development not readily acquired during class hours,
e.g. performing calculations or balancing chemical equations. Assignments are usually taken from the textbook, so students
are obliged to have their own copy by purchase or rental.
Web-based Materials: In addition to lecture notes and textbook, the following are
available via the web: structures, functions, and molecular visualizations. These can be
found in the web page addresses specified in the textbook and sometimes given by the
instructor. Clarifications and short tutorial-consultations may be called to the instructor’s
attention thru email (address given above) provided that the student will give his/her
complete identification.
Other Activities: Depending
on the availability of facilities, some class periods may be
spent in the AVR for other instructional
modes like video-showing or PowerPoint
presentations or multi-media activities.
Class Decorum:
Students are expected to be present in all class periods. Allowed number of absences will be accounted according to
school policy for the current semester. Tardiness is not also tolerated. Taking of lecture notes is an integrated function
of every student as well as studying and participating in class
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