CHEM 738 : Biomolecular Chemistry


2022 Semester Two (1225) (15 POINTS)

Course Prescription

Discusses how techniques including NMR spectroscopy, calorimetry, neutron scattering and computational modelling, can characterise the molecular structure, dynamics, and interactions of biological macromolecules. The principles of each technique will be presented and complemented with examples of where these methods have made major advances in understanding important biochemical processes. Accessible to students with a background in chemistry, biology, bioengineering, or physics.

Course Overview

This course is designed to prepare graduate students to work at the chemistry and biology interface, with a focus of applying biophysical and computational techniques to study macromolecules (such as proteins). This course is useful for students who want to pursue a PhD in biological chemistry, medicinal chemistry, biochemistry, chemical biology, structural biology, computational chemistry or enzymology, as well as those who wish to move to industry (e.g. pharmaceutical industry, biotechnology industry) after they graduate. No specific prerequisites are required for this course, but some background in chemistry or biology is useful.

Course Requirements

No pre-requisites or restrictions

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: Master of Science

Learning Outcomes

By the end of this course, students will be able to:
  1. Apply the appropriate NMR technique to study protein-ligand interactions, to measure protein dynamics at different timescales, and to solve the three-dimensional structure of proteins. (Capability 1, 2, 3 and 5)
  2. Use NMR software to analyse protein NMR data. (Capability 1, 2, 3 and 5)
  3. Summarise independently, discuss, critically evaluate and provide feedback about scientific literature that is related to the discipline of protein NMR. (Capability 1, 2, 3, 4, 5 and 6)
  4. Summarise the major components of a typical cell membrane and to explain their function within the broader framework of the cell membrane function, to assess the current model of the cell membrane and to identify uncertainties in the current state of knowledge. (Capability 1, 2, 3, 4 and 5)
  5. Define different methods of producing a model system that represents a cell membrane in vitro, to critically assess the advantages and disadvantages of different model systems and to identify appropriate model systems to employ for different characterisation problems. (Capability 1, 2, 3, 4 and 5)
  6. Summarise different imaging techniques that can be used to characterise components of a cell membrane, to critically evaluate the advantages of different imaging methods and to independently evaluate and prepare a proposal for an imaging experiment. (Capability 1, 2, 3, 4 and 5)
  7. Conduct BLAST searches comparing amino acid residue sequences using the relevant on-line software. (Capability 1, 2, 3 and 5)
  8. Identify the relevant homology models from different repositories depending on the protein system under investigation. (Capability 1, 2, 3 and 5)
  9. Utilise a wide range of computational tools useful to model the structure, dynamics and association of biological molecules. (Capability 1, 2, 3 and 5)


Assessment Type Percentage Classification
Final Exam 50% Individual Examination
Assignments 50% Individual Coursework
Assessment Type Learning Outcome Addressed
1 2 3 4 5 6 7 8 9
Final Exam

Key Topics

Molecular structure and motion: An introduction to protein nuclear magnetic resonance (NMR) spectroscopy, with particular focus on protein-ligand interactions, the elucidation of protein structures, and the studies of protein dynamics. 
Cellular membranes: An introduction to the composition and properties of cellular membranes, and their interactions with membrane proteins. A description of methods of studying cellular membranes and other biological interfaces, with a focus on neutron and X-ray scattering techniques. 
From Sequence to Structure and Dynamics: Following up on the lecture content covered by Dr Arabshahi, the lectures of Dr Mercadante will provide an overview on how the theoretical framework of molecular mechanics can lead to the estimation of molecular dynamics. The lectures will provide an introduction to molecular dynamics simulations and to all the observables, obtained from sampling molecular dynamics via computational methods, that relate to molecular function. Lectures will be followed by tutorials in which the students will take on the preparation of a molecular dynamics simulation of a protein and its analysis. Such tutorials will provide the students with rudimental skills in python scripting to explore molecular structures and dynamics.

Special Requirements


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 24 hours of lectures/tutorials, and 96 hours of reading and thinking about the content and work on assignments and examination preparation.

Delivery Mode

Campus Experience

Attendance is expected at scheduled activities including tutorials to complete components of the course.
Lectures will be available as recordings. Other learning activities including tutorials will not be available as recordings.
Attendance on campus is required for the exam.
The activities for the course are scheduled as a standard weekly timetable.

Learning 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.

Learning material will be provided on CANVAS.

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.

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.

Class Representatives

Class representatives are students tasked with representing student issues to departments, faculties, and the wider university. If you have a complaint about this course, please contact your class rep who will know how to raise it in the right channels. See your departmental noticeboard for contact details for your class reps.


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 course assessment continues to meet the principles of the University’s assessment policy. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator/director, and if disruption occurs you should refer to the university website for information about how to proceed.

The delivery mode may change depending on COVID restrictions. Any changes will be communicated through Canvas.

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 students may be asked to submit 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. In exceptional circumstances changes to elements of this course may be necessary at short notice. Students enrolled in this course will be informed of any such changes and the reasons for them, as soon as possible, through Canvas.

Published on 10/11/2021 07:12 p.m.