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Compulsory/Elective
Required textbooks
and course materials
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Course objectives
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(code, title,
credits)
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(undergraduate,
graduate)
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Bioorganic CHEMISTRY (3 credits)
Biomedical Engineering
Undergraduate
FALL 2015
Dr. Jestin Mandumpal
[email protected] or [email protected]
+994 514142095
This course is a prerequisite for the Course Biochemistry studied further
English
compulsory
Core textbooks
1. Organic Chemistry A Brief Course, Robert C. Atkins & Francis A.
Carey
2. Organic Chemistry T.W. Graham Solomons
This course is based on traditional face-to-face classes
Alcohols, Ethers and Phenols/ Aldehydes and Ketones/Carboxylic acids &
their derivatives/ Amines/Carbohydrates/Amino acids, Peptides, and
Proteins/Lipids/Nucleic acids
This course is a prerequisite for the Course Biochemistry  studied further.
General Objective of the Course
To meet curriculum requirements of the School of Architecture, Engineering
and Applied Sciences.
Specific Objectives of the Course
-To support student academically, to improve their chances of realizing their
potential.
-To encourage students participation and interaction as well as fostering
atmosphere of tolerance and respect.
-To develop understanding the fundamentals of chemistry.
-To build background for the students further studying Biochemistry 
By the end of the course the students should be able
-To know and apply main laws of chemistry.
-To know properties of the main chemical elements and their most important
compounds.
-To know properties of the most important organic & biorganic compounds.
x
Lecture
x
Group discussion
Experimental exercise
Case analysis
Simulation
x
Course paper
Others
Methods
Date/deadlines
Percentage (%)
Policy
November, 2014
30
Midterm Exam
20
Assignment and
quizzes
10
Presentation/Group
Discussion
May, 2015
40
Final Exam
100
Total
Attendance
The students are required to attend all classes as a part of their studies and
those having legitimate reasons for absence (illness, family bereavement, etc.)
are required to inform the instructor.
Tardiness / other disruptions.
If a student is late to the class for more than 10 (ten) minutes, (s)he is not
allowed to enter and disturb the class. However, this student is able to enter
the second double hours without delaying.
Exams
In order to be excused from the exam, the student must contact the dean and
the instructor before the exam. Excuse will not be granted for social activities
such as trips, cruises and sporting events (unless you are participating). The
exams will all be cumulative. Most of the questions on each exam will be
taken from the chapters covered since the last exam.
But some will come from the earlier chapters. In general the coverage will
reflect the amount of the time spend in class on the different chapters.
Withdrawal (pass / fail)
This course strictly follows grading policy of the School of Engineering and
Applied Sciences. Thus, a student is normally expected to achieve a mark of
at least 60% to pass. In this case of failure, he/she will be referred or required
to repeat the course the following term or year.
Cheating / plagiarism
Cheating or other plagiarism during midterm and final examinations will lead
to paper cancellation. In case, the student will automatically get 0 (zero),
without any considerations.
Professional behaviour guidelines
The student shall behave in the way to create favorable academic and
professional environment during the class hours. Unauthorized discussions
and unethical behavior are strictly prohibited.
For successful completion of the course, the students shall take an active part
during the class time, raising questions and involving others to discussions.
Learning and Teaching Methods
This course considers active learning process rather than passive one.
Week
Topic
1
1
Tentative Schedule
Topics
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
ix.
x.
xi.
xii.
2
2
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
3
2
ix.
x.
xi.
xii.
xiii.
xiv.
xv.
xvi.
xvii.
Alcohols, ethers and Phenols (272303)
Alcohols a review (273)
Natural resources of alcohols (275)
Preparations of alcohols (276)
Alcohols as BrØnsted acids(281)
Oxidation of alcohols(282)
Introduction to Ethers (286)
Preparations of Ethers & Epoxides
(290)
Naturally occurring Phenol derivatives
(294)
Acidity of Phenols (295)
Reactions of Phenols. Preparation of
Aryl Ethers(297)
Oxidation of Phenols. Quinones (298)
Review of the topic
Aldehydes and Ketones (308−346)
Structure and Bonding of the Carbonyl
group (311)
Physical Properties (313)
Sources of Aldehydes and Ketones
(313)
Preparation of Aldehydes and Ketones
(314)
Reactions of Aldehydes and
Ketones(317)
Hydration of Aldehydes and Ketones
(318)
Acetal formation(320)
Cyanohydrin Formation(322)
Reactions with Derivatives of
Ammonia (324)
Reactions that introduce new CarbonCarbon bonds (325)
Grignard Reagents (327)
Synthesis of Alcohols using Grignard
Reagents(328)
Grignard Reagents in synthesis.
Working Backward(330)
The alpha Carbon and its Hydrogens
(332)
Enols and Enolates (333)
The Aldol condensation(335)
Oxidation of aldehydes (338)
Textbook/Assignments
[1]
[1]
[1]
4
3
Carboxylic acids (347-365)
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
5
6
4
4
Carboxylic acid derivatives (366-397)
i.
Nomenclature of Carboxylic acid (367)
ii.
Acyl Transfer reactions : Hydrolysis
(368)
iii.
Natural sources of Esters (370)
iv.
Preparation of Esters: Fischer
Esterification (371)
v.
Preparation of Esters(374)
vi.
Reactions of Esters (375)
vii.
Polyesters (377)
viii.
ix.
x.
xi.
xii.
xiii.
7
5
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
8
5
Carboxylic acid nomenclature (348)
Physical Properties (349)
Acidity of Carboxylic acids (350)
Substituents and acid strength(351)
Salts of Carboxylic acids(353)
Sources of carboxylic acids (355)
Preparation of Carboxylic acids (357360)
Reactions of Carboxylic acids (360)
Reactions of Esters with Grignard
reagents(380)
Natural sources of amides (383)
Preparation of amides (383)
Hydrolysis of amides (386)
Polyamides (387)
review
Amines (398−424)
Amine Nomenclature (399)
Structure and Bonding (401)
Physical Properties (402)
Amines in nature (403)
Amines as bases (404)
Preparation of alkylamines by
alkylation of ammonia (406)
Preparation of alkylamines by
reduction (407)
Preparation of arylamines(408)
Reactions of amines (409)
Reactions of Amines with Alkyl
Halides (410)
xi.
The Hoffmann Elimination (411)
xii.
Nitrosation of Amines (413)
xiii. Reactions
of
Aryl
Diazonium
salts(415)
xiv. Azo dyes (417)
Midterm exam :: topics 1 − 5
[1]
[1]
[1]
[1]
ix.
x.
[1]
9
6
10
6
Carbohydrates (425−449)
i.
Classification (426)
ii.
Glyceraldehyde and the D-L system
of steroechemical notation (426)
iii.
The aldotetroses (428)
iv.
Aldopentoses and Aldohexoses (429)
v.
Cyclic Forms of Carbohydrates :
Furanose forms(431)
vi.
Cyclic forms of Carbohydrates :
Pyranose forms(434)
vii.
Hemiacetal equilibrium(435)
viii. Ketoses(436)
[1]
ix.
x.
xi.
xii.
xiii.
xiv.
xv.
11
7
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
ix.
x.
xi.
xii.
xiii.
12
[1]
8
Structural variations in Carbohydrates
(438)
Glycosides(439)
Disaccharides (440)
Polysaccharides (442)
Oxidation of Carbohydrates (443)
Osazone formation (444)
Review
Amino acids, Peptides and Proteins
(451-476)
Structure of Aminoacids (451)
Stereochemistry of Amino acids(454)
Acid-Base behaviour of Amino acids
(455)
Synthesis of Amino acids (456)
Peptides (457)
Peptide structure determination (460)
End group analysis: N and C terminus
(461-463)
Selective Hydrolysis of Proteins (463)
The strategy of Peptide Synthesis
(464)
Protecting groups and peptide bond
formation (465)
Secondary structures of peptide and
proteins (466)
Tertiary structure of peptides and
proteins (470)
Protein
Quaternary
structure
Haemoglobin (471)
Lipids (477-496)
i.
ii.
iii.
iv.
v.
vi.
Classification of Lipids (478)
Fats and Fatty Acids (478)
Phospholipids (480)
Waxes (482)
Steroids, Cholesterol (482)
Vitamin D (483)
[1]
[1]
13
8
14
9
vii.
viii.
Bile Acids (485)
Corticosteroids (486)
ix.
x.
xi.
xii.
xiii.
Sex hormones (486)
Biosynthesis (488)
Terpene Biosynthesis (489)
Iospentenyl Pyrophosphate (492)
Review of the topic (477-494)
[1]
[1]
vii.
Nucleic Acids (497- 510)
Pyraimidines and Purines (497)
Nucleosides (498)
Nucleotides (500)
Nucleic Acids (501)
Structure and Replication of DNA The
Double helix (502)
DNA-Directed Protein Biosynthesis
(507)
Review of the topic
i.
Review of the topics ( 5-9)
i.
ii.
iii.
iv.
v.
vi.
15
January 2016
Final exam :: topics 5-9
This syllabus is a guide for the course and any modifications to it will be announced in advance.