CHEM 351 : Chemicals Big and Small: Nano-material to Bio-macromolecules


2021 Semester One (1213) (15 POINTS)

Course Prescription

Chemical materials are found with a broad range of shapes, sizes and physical properties. Students will study the synthesis of chemical materials; including polymeric materials using radical chemistry, inorganic materials and proteins and peptides using synthetic and biological chemical approaches. Methods to characterise materials will be investigated, including a range of physical and computational techniques giving insight into molecular interactions.

Course Overview

Block 1: Physical and Computational Chemistry: An introduction to current methods in computational chemistry and molecular modelling
Block 2: Polymer Chemistry: Polymeric materials, synthesis techniques (esp. the free radical chemistry and its use for free radical polymerisation), polymerization kinetics, polymer characterization and applications.
Block 3: Bio-molecules; Molecular Self-Assembly: Carbohydrates, Amino Acids, Solid Phase Peptide Synthesis, Structural Organisation in Proteins, HIV protease and inhibitors, Molecular Self-Assembly (self-assembling peptides), Functions of these molecules.
Block 4: Chemical Biology: Recombinant Protein Production; Chemistry and Synthesis of Nucleic Acids; Serine Protease and Glycosydase: Mechanism and Kinetics; Target Identification; Emerging Topics in Chemical Biology.

Course Requirements

Prerequisite: 30 points from CHEM 251, 252, 253 Restriction: CHEM 350

Capabilities Developed in this Course

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
Graduate Profile: Bachelor of Science

Learning Outcomes

By the end of this course, students will be able to:
  1. Apply computational modelling for molecules and reactions using various specialized software packages (Graduate Profile Capabilities used: 1, 2, 3) (Capability 1, 2 and 3)
  2. Describe various methods to synthesise and characterise polymers and outline the various applications of polymeric materials (Graduate Profile Capabilities used: 1, 2, 3, 6) (Capability 1, 2, 3 and 6)
  3. Use and apply the principles of radical reactions and describe various radical reactions in organic and polymer synthesis and biological systems (Graduate Profile Capabilities used: 1, 2, 3, 6) (Capability 1, 2, 3 and 6)
  4. Describe and discuss various methods for the synthesis, analysis and modification of carbohydrates, peptides/proteins and biomolecules, including those featuring metals (Graduate Profile Capabilities used: 1, 2, 6) (Capability 1, 2 and 6)
  5. Communicate results of laboratory and computational analysis in various ways including in forms for a non-technical audience. (Graduate Profile Capabilities used: 1, 2, 4, 5) (Capability 1, 2, 4 and 5)


Assessment Type Percentage Classification
Test 15% Individual Coursework
Laboratories 25% Individual Coursework
Assignments 10% Individual Coursework
Quizzes 5% Individual Coursework
Tutorials 5% Individual Coursework
Final Exam 40% Individual Examination
Assessment Type Learning Outcome Addressed
1 2 3 4 5
Final Exam


Key Topics

Topic 1: An introduction to current methods in computational chemistry and molecular modelling
• Background on theoretical and computational methods used in molecular modelling.
• Understanding of the capabilities, limitations and reliability of various computer based methods
• Application of computation chemistry in different areas of chemistry including drug discovery projects case studies
Topic 2: Polymer Chemistry and Kinetics
Polymers along with metal and ceramic are the three major materials in today’s world. Overall, this topic is to introduce students a basic understanding of polymeric materials, its synthesis techniques (especially radical chemistry and its use in free radical polymerisation), polymerization kinetics, polymer characterization and applications.
• Develop an understanding of what are polymers and their use in human history, the importance of polymers in human survival and civilization advancement, polymer nomenclature, polymer size, long chain conformation, molecular weight in polymers and molecular weight distribution, polymer classification
• Develop a deeper understanding of free radical chemistry and free radical polymerization to make polymers, radical polymerization kinetics, chain transfer and termination processes, degree of polymerization control, multiple radical species for radical co-polymerization kinetics.
Topic 3: Carbohydrates, Amino Acids, Peptides and Proteins, Molecular Self-Assembly
Carbohydrate chemistry
• Basics of carbohydrate Chemistry including classification, D and L sugars based on Fischer projections.
• Common reactions that have implications in carbohydrate structures such as hemiacetal formation as an intramolecular cyclization reaction, formation of anomers and mutarotation and concept of reducing and non‐reducing sugars.
• Be able to apply the carbonyl and amine chemistry in the context of monosaccharides. general reactions including glycoside chain lengthening and shortening reactions.
• Basic understanding of the structure of disaccharides – recognize the glycosidic bond in disaccharides, be able to classify given disaccharide structures as reducing or non‐reducing with reasoning.
• Describe simple aspects of the structures and properties of polysaccharides such as cellulose, starch, glycogen.
Amino acids, peptides and proteins
• Organisation of proteins starting from amino acid building blocks, structure of α-amino acids, and their zwitterionic nature, isoelectric points and understand the importance of amino acid side chains in the formation of peptide secondary structures and protein folding. Primary, secondary, tertiary and quaternary structure in proteins
• Deduce the chirality of amino acids and understand the influence of on amino acid protonation states.
• Apply the chemistry covered in CHEM 253 (amines and carbonyl compounds) to the synthesis of α-amino acids and other important reactions for amino acid syntheses. (e.g. HVZ, Strecker, Amidomalonate, reductive amination).
• To describe in a qualitative sense details of peptide structure (peptide bond, disulphide bond)
• Draw mechanisms for the synthesis of amide bonds in the context of amino acids, including the use of coupling agents and protecting groups.
• Ramachandran Plot and Peptide Conformation
• Synthetic Conformational Restrictions in Peptides – Cyclic Peptides, Peptidomimetics and the use of non-protein amino acids
• Amino acid analysis, including peptide sequencing reactions.
• HIV protase as a drug target and the design and mechanism of action of HIV protease inhibitors
• Describe the role of the hydrolytic enzyme carboxypeptidase A, the details of the active site of the enzyme and how the interplay of the zinc ion and the surrounding proteins leads to facile hydrolysis of amide bonds.
Topic 4: Other Biomolecules (not Covered in Topic 3) and including biomolecules involving metals
• Discussing the process of turning biomolecular monomers to biopolymers; from amino acids to proteins, simple to complex carbohydrates and nucleotides to nucleic acids
• Production of biomolecules - recombinant protein production
• Production of biomolecules - solid phase nucleic acid synthesis
• Enzyme mechanism and enzyme kinetics including serine protease and glycosidase
• Application of chemistry in biology - target identification, photoaffinity labelling and protein identification (using electrophoresis / mass spectrometry)
• Chemistry of nucleic acids (compound stability, importance of pKa, driving forces in nucleic acid chemistry)
• Epigenetics ( Nature vs nurture and posttranslational modification)
• Regulation of gene expression (Knockout / knockdown and CRIPSR-Cas9)
• Use the general principles of coordination chemistry to explain in a qualitative way the mechanism of action of selected biomolecules
• Describe the role of siderophores in biological systems, the structures of siderophores, the main features of the chemistry involved in the iron sequestering process, model compounds.
• Describe the mode of action of the Na+/K+ ion pump and the role it plays in cell function. Describe the chemistry involved in the action of the pump and the relatively simple molecular compounds that model the ion selectivity properties of the pump.
• Describe the essential features of the coenzyme vitamin B12, the types of transformations that are catalysed by the holoenzymes that are formed by combination this co-enzyme with the appropriate apoenzymes, the coordination environment of the cobalt atom at the active site in coenzyme B12 and details of the mechanism by which this co-enzyme operates.

Special Requirements

Must complete laboratory/practical work and comply with all health and safety regulations whilst in the 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 32 hours of lectures, 20 hours of reading and thinking about the content and 37 hours of work on assignments and/or test preparation.

Delivery Mode

Campus Experience

Campus Experience

Attendance is required at scheduled activities including labs/tutorials to receive credit components of the course.

Lectures will be available as recordings. Other learning activities including tutorials/labs will not be available as recordings.

The course will not include live online events including [group discussions/tutorials].

Attendance on campus is required for the test.

The activities for the course are scheduled as a standard weekly timetable.

Learning Resources

All course material will be available on Canvas. This includes lecture recording links and videos of laboratory techniques.

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.

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.

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.


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.

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

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

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

Learning Continuity

In the event of an unexpected disruption we undertake to maintain the continuity and standard of teaching and learning in all your courses throughout the year. If there are unexpected disruptions the University has contingency plans to ensure that access to your course continues and your assessment is fair, and not compromised. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator, and if disruption occurs you should refer to the University Website for information about how to proceed.

The delivery mode of this course may change in accordance with changes to New Zealand Government recommendations. Updates for this course will be provided on the course Canvas page.
Level 1: All main teaching activities will be conducted on campus and in person.
• Lectures: on campus, recorded lectures will be available.
• Labs, tutorials: on campus, remote versions will not be available.
• Tests, exams: on campus, you must attend in person unless you are unwell or other circumstances outside your control prevent you from attending. You must complete the exam to pass the course.
Level 2: Some teaching activities will be conducted on campus with remote versions available
• Lectures: delivered remotely, available at the timetabled time and recorded lectures will be available.
• Labs, tutorials: on campus, remote versions will be available.
• Tests and quizzes: delivered remotely at timetabled time.
• Exams: delivered remotely at timetabled time. You must complete the exam to pass the course.
Level 3/4: All teaching activities are remote
• Lectures, labs and tutorials: delivered remotely, available at the timetabled time and recordings of the sessions/online versions will be available.
• Tests and quizzes: delivered remotely at timetabled time.
• Exams: delivered remotely at timetabled time. You must complete the exam to pass the course.
This course may be taken remotely, including tests and exams, if you meet Ministry of Health guidelines and receive an exemption, or are unable to attend because of border restrictions. 

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


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.

Published on 18/06/2021 10:55 a.m.