CHEM 110 Chemistry of the Living World - Course Outlines

Course Prescription

A foundation for understanding the chemistry of life is laid by exploring the diversity and reactivity of organic compounds. A systematic study of reactivity focuses on the site and mechanism of reaction including application of chemical kinetics. A quantitative study of proton transfer reactions features control of pH of fluids in both living systems and the environment. It is recommended that students with a limited background in chemistry take CHEM 150 prior to CHEM 110.

Course Overview

In this course, you will be introduced to the chemical language and concepts underpinning all study in the life sciences. The focus of the course is on developing a chemical vocabulary and chemical reasoning that can be applied to a range of scientific disciplines, especially biology, pharmacology, physiology, medicine and pharmacy. We will discuss how chemical language is used and misused in the public sphere, equipping you to use your chemistry knowledge outside the class setting. A deeper coverage of organic reaction mechanisms, principles of chemical kinetics and acid/base chemistry will support students wishing to progress in the chemical sciences.

This course assumes knowledge of the NCEA3 chemistry syllabus (or equivalent), particularly the external credits. Students who have completed less that 2/3 of the external credits, or did not take chemistry in their final year (IB, Cambridge) should take CHEM150 prior to enrolling in CHEM110. Where this is not possible due to program requirements students may wish to consider a preparatory course, for example BestChoice Prep Chem Online, prior to starting CHEM110.

Course Requirements

No pre-requisites or restrictions

Learning Outcomes

By the end of this course, students will be able to:

Identify and describe the chemical reactivity and physical properties of organic compounds using scientific vocabulary and drawing conventions. (Capability 1 and 4)
Predict physical properties and chemical behaviour of organic molecules based on their physical and/or electronic structure. (Capability 1 and 3)
Use spectrophotometric information to identify organic molecules. (Capability 1 and 3)
Recall principles of chemical kinetics, and relate these to concepts of reaction mechanisms. (Capability 1)
Describe and explain principles of acid-base behaviour. (Capability 1)
Perform appropriate mathematical manipulations on data to solve problems. (Capability 1 and 3)
Follow experimental protocols, including safety procedures, to prepare and analyse organic compounds. (Capability 1 and 5)
Critically analyse chemistry reporting in the news, and discuss issues in science reporting with a non-scientific audience. (Capability 2, 4, 5 and 6)

Assessments

Assessment Type	Percentage	Classification
Test	15%	Individual Test
Quizzes	5%	Individual Coursework
Laboratories	15%	Individual Coursework
Assignment	15%	Individual Coursework
Final Exam	50%	Individual Examination
5 types	100%

Assessment Type	Learning Outcome Addressed
	1	2	3	4	5	6	7	8
Test
Quizzes
Laboratories
Assignment
Final Exam

Tuākana

Tuākana runs dedicated tutorials for this course, based around worksheets designed specifically for the course. Tuākana may run additional activities at the request of students in the group. Tuākana students enrolled in chemistry are welcome to use the chemistry tuākana space at any time during normal business hours.

Key Topics

Foundations: Bonding, drawing structures, functional groups, nomenclature, isomerism, reaction classification and electron movement.
Spectroscopy and Structure Determination: Mass spectrometry. Ultraviolet- visible, infrared and nuclear magnetic resonance spectroscopy.
Kinetics: Rate laws, integrated rate laws, Arrhenius Equation, rate laws and mechanism, applications of chemical kinetics.
Functional Group Chemistry I: Alkenes, alkynes, aromatics and alkyl halides.
Acids and Bases: Speciation, pH, Ka and pKa, titrations.
Functional Group Chemistry II: Alcohols, aldehydes and ketones, carboxylic acids & derivatives, amines and peptides & proteins, carbohydrates and radicals.

Learning Resources

The CHEM110 course folder is required for all students and can be purchased from the Science Resource Centre. This contains the shell of the lecture notes as well as the laboratory manual. A pdf copy is available for students who use a tablet with annotation capabilities. Students need to bring a copy of the course folder to lectures that they can annotate both with drawings and writing.

The recommended textbook for the course is Blackman's Chemistry (3rd or 4th Ed.). This is supplementary reading (not required reading) and is particularly encouraged for students without a strong background in chemistry at NCEA3 (or equivalent).

All other resources, including a CHEM110 specific site subscription to BestChoice, will be provided free of charge to students via Canvas.

Special Requirements

Attendance at laboratories is a compulsory part of this course. Students who miss more than one lab (without a formal excusal) or two labs (with formal excusals) will not be eligible to pass the course. Wearing of a laboratory coat, covered footwear and suitable eye protection (e.g. safety glasses) is compulsory at all times when present in the laboratory. If a student does not wear adequate eye protection, appropriate footwear or a laboratory coat at all times, the student will be asked to leave the laboratory and will receive a fail for that laboratory.

Workload Expectations

This course is a standard 15 point course and students are expected to spend 10 hours per week involved in each 15 point course that they are enrolled in.

For this course, you can expect 6 hours of lectures, a 3 hour laboratory, 6 hours of reading and thinking about the content and 5 hours of work on assignments and/or test preparation per fortnight, and additional preparation during the exam period.

Other Information

Detailed Course Description:

Organic compounds of interest to chemists, biologists and those studying and researching in all areas of medicine and health sciences range from the structurally simple to the very complex. Fortunately organic compounds can be classified into a relatively small number of structurally similar groups. Similarity in structure means similarity in physical properties and often reactivity. Thus a reasonable approach to providing a sound basis for an understanding of organic molecules is to commence with the simplest organic molecules, identify their common features, and gradually progress to more complex molecules.

1.1 INTRODUCTION and FOUNDATIONS (~7 lectures) Structure and bonding in organic molecules. Functional groups and their nomenclature. Isomerism: Constitutional and conformational. Configurational isomerism in relation to alkenes (E-Z nomenclature) and cycloalkenes. Chirality and optical activity. R and S convention. Bonding and reactions: Electronegativity, bond polarity and physical properties. Chromatography. Homolytic and heterolytic bond breaking and bond making. Intermediates and reaction classifications.

1.2 FUNCTIONAL GROUP CHEMISTRY (~14 lectures) Alkenes: Synthesis from alkyl halides and alcohols; catalytic hydrogenation. Additions initiated by addition of proton, stability of alkyl substituted carbocations; bromine, stereochemistry and the bromonium ion. Alkynes: Synthesis from vinyl halides and by nucleophilic substitution using acetylide anions. Catalytic hydrogenation, complete and partial. Electrophilic additions. Aromatics: The structure of benzene and resonance energy. Electrophilic aromatic substitutions; bromination, chlorination, nitration, alkylation and acylation of benzene; activation and deactivation; ortho‐ para- and meta‐ directors. Phenols: From benzenediazonium salts. Acidity. Alkyl halides: Bromides and chlorides by HX addition to alkenes and HX substitution of alcohols. SN1 and SN2 reaction mechanisms; stereochemistry. E1 and E2 competing with SN; stereochemistry. Preparation of organometallic halides. Ethers: From alkyl halides and alcohols or phenols. Alcohols: From alkenes, alkyl halides, aldehydes, ketones and esters. Amphoteric nature of alcohols. Substitution and elimination reactions. Grignard synthesis. Aldehydes and ketones: Properties of the C=O bond. Synthesis by acylation of aromatic rings, oxidation of alcohols. Nucleophilic addition of NaBH4, RMgX, ROH, H2O. Hemiacetals and acetals. Carboxylic acids: Preparations by oxidation of alcohols, aldehydes and aliphatic side-‐chains; by carboxylation of organometallic halides and by nitrile hydrolysis including cyanohydrins. Relative acidities of carboxylic acids. Carboxylic acid derivatives: Acyl halides, anhydrides, esters, amides and nitriles, their hydrolysis and interconversions. Nucleophilic acyl substitution. Ester reactions with RMgX, LiAlH4. Amines: Synthesis from alkyl halides and ammonia; from imines, amides, nitrile and nitro compounds. Base strength and reactions as nucleophiles. Quaternary ammonium salts. Aromatic amines; synthesis by reduction of ArNO2 and benzenediazonium ions. Amino acids: structures, structure in acidic, neutral and basic solutions, configuration, reactions to form peptides including the use of protecting groups, structure and function of proteins using enzymes as examples. Carbohydrates: Configuration of monosaccharides, cyclic structures of monosaccharides, monosaccharide anomers and mutarotation. Reactions of monosaccharides.

1.3 SPECTROSCOPY (4 lectures) Mass spectrometry and the molecular ion. Ultraviolet-visible, its use in detecting π bonds and conjugated systems and Beer’s Law. Infrared and 13C and 1H nuclear magnetic resonance. Use of spectroscopic methods to identify specific structural units present in molecules, and structure determination of molecules.

2.1 KINETICS (4 lectures) Definition and measurement of reaction rates; qualitative effects of concentration, temperature and catalysts on reaction rates; reaction order and rate laws; integrated rate laws in simple systems; Arrhenius equation and activation energy, interpretation in terms of collision theory; reaction mechanisms, rate‐limiting steps, intermediates and transition states; common organic reaction mechanisms and rate laws; catalysis and enzymes; design of reaction conditions for desired outcome based on kinetic concepts.

2.2 ACIDS AND BASES (4 lectures) Definition of acids and bases, proton transfer reactions; strengths of acids, Ka and pKa; relation of acid strength to structure; pH and species present in acid/base/salt solutions; titration curves and indicators; buffer solutions and applications; role of very strong acids and bases in organic chemistry; effect of pH on charged species (especially biological molecules), electrophoresis; acid rain, soil chemistry and pH, pH and colour in biological systems.

Digital Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.

Lecture recordings are intended to supplement (not replace) lectures. Technical issues with recordings, including delays in posting the recording, will never be considered grounds for an extension or special consideration on any piece of assessed work.

Copyright

The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed against online source material using computerised detection mechanisms.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website at http://disability.auckland.ac.nz

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page: https://www.auckland.ac.nz/en/students/academic-information/exams-and-final-results/during-exams/aegrotat-and-compassionate-consideration.html.

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter (https://www.auckland.ac.nz/en/students/forms-policies-and-guidelines/student-policies-and-guidelines/student-charter.html).

Disclaimer

Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course you may be asked to submit your coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. The final decision on the completion mode for a test or examination, and remote invigilation arrangements where applicable, will be advised to students at least 10 days prior to the scheduled date of the assessment, or in the case of an examination when the examination timetable is published.

Capability 1:	Disciplinary Knowledge and Practice
Capability 2:	Critical Thinking
Capability 3:	Solution Seeking
Capability 4:	Communication and Engagement
Capability 5:	Independence and Integrity
Capability 6:	Social and Environmental Responsibilities

CHEM 110 : Chemistry of the Living World

Science

2020 Semester Two (1205) (15 POINTS)