No required text.  Background readings from co-requisite CBMS102 and CBMS103 may be required. You will be required to shoot 2 videos as part of this unit.

Lectures in Semester 1 will be Tuesday 1-2PM in E7B346 (200-300-level chemistry lab write-up room)

Semester 1

Wk 1:No Lecture.  Download unit guide, familiarise yourself with the curriculum and expectations and participate in virtual meeting on the CBMS188 web site.

Wk 2-5 LB

This four-week section will introduce you to the chemistry of biological macromolecules, particularly proteins. You will gain an understanding for why the bigger a molecule becomes, the more difficult it is to determine its structure. We will look at several novel approaches at the forefront of determining structures of biological macromolecules. We will also focus on several classes of proteins including molecular motors, light receptors and channels.  We will dissect mechanisms behind how and why proteins can move and change shapes to perform their required functions.

Wk 2: Introductory remarks and overview of the unit. Introduction to properties of amino acids and protein folding.  Explore conventional structural methods, including X-ray crystallography and NMR spectroscopy. Discussion on several notable biomacromolecules including examples of molecular motors, fluorescent proteins, membrane proteins Pick your own 'biomacromolecule'.

Wk 3: Introduction to primary literature for researching your chosen biomacromolecule. Group Task - Plan your YouTube video for filming in week 12.

Wk 4: Group task– film your YouTube video in small groups

Wk 5: Group presentations of your YouTube videos of your selected biomacromolecule. Discussion/Debate of the definition of chemistry and whether 'structural biology' can indeed be classified as chemistry.

Wk 6: Hand in your individual written report

Wk 6-9 DW

In this section, we will firstly extend principles of redox reactions already developed in high school chemistry, followed by their applications to analytical detection.  More specifically, we will direct our attention to how electrochemistry is applied to modern development of sensitive and selective sensing technologies.  This section build on Brown Ch 19 and involves some theory and a laboratory experiment will be conducted, led by your third year mentor, to enhance understanding of principles presented in this section, as well as to gain hands-on experience of some advanced electroanalytical detection techniques. Students will then be required to deliver a verbal presentation of their independent research on selected sensor development and a formal lab report, which is graded.

Wk 6: Review of basic electrochemistry; Hand in your individual written report for LB

Wk 7: Laboratory work

Wk 8: Discussion of results

Wk 9: Oral presentation and hand in lab report

Wk 10-13 IJ

Chemical gardens are the plant-like structures formed when a soluble metal salt in the form of a seed crystal is placed in an aqueous solution, typically, sodium silicate. Tubular structures form, rising up from the seed crystal. This process has some parallels with other precipitation processes, such as  the huge black “smokers” that grow up to 30 m tall at hydrothermal vents on the ocean’s floor. At smaller length scales, it causes the growth of beautiful “soda-straw” stalactites in limestone caves. We will explore the chemistry of the formation of these crystal gardens and use the technique of “slowmation” to document the process. The topics covered are an extension of CBMS102 (corequisite) and cover; transition metal salts (colours of as arising from electronic transitions, bonding of, geometry of), precipitation reactions, diffusion, osmosis and semi-permeable membranes. These are extensions of Brown Ch 1 (Modern Atomic Theory), Ch 3 (Stoichiometry) Ch 5 (Chemical Bonding), Ch 9 & 10 (Chemical Equilibrium; particularly "Ionic Equilibria" & solutions/solubility) and Ch 13 (Coordination Chemistry) presented in an integrated, holistic fashion.

Wk 10: Lecture on dissolution, precipitation, diffusion and osmosis with regards to the crystal gardens and electronic structure, including crystal field theory, of transition metal salts

Wk 11: Grow Crystal Gardens in the lab. Make photographic record

Wk 12: Class discussion. Construct webpage

Wk 13: Presentation of web page and 1st draft of essay

Wk 14: Hand in your essay

Wk 15: Examination week (CBMS188 has no mid-year exam)

Semester 2

Wk 16:             introduction to SciFinder Scholar by your 3rd year mentors (in 200/300-level chem labs)

  Week 2-5 FL

This section of the course will provide you with an overview of more advanced concepts in chemical bonding and structure, chemical and physical principles behind molecular recognition, and their applications in fundamental discoveries. This section is an extension of CBMS103 as it deals with more advanced theories on bonding, structures, conformations, H-bonds, and reaction energy controls. These are extensions of McMurry Ch. 1, 2, and 3 (Structure and bonding, nature of organic molecules, and nature of organic reactions).  Specific topics include:

Wk 17:  Localised and delocalised bonding: From Lewis to Schrödinger

Wk 18:  Weak bonding interactions behind strong networks

Wk 19:  Recognition motifs of the molecular world

Wk 20:  Time-dependent chemical complexity

Wk 21 hand in take-home exam

Week 6-9 PK

This section of the course will provide you with an overview of Chemical Diversity, Combinatorial Chemistry and more advanced aspects of organic chemistry mechanisms that can lead to Diversity Orientated Synthesis. Topics covered are extension of McMurry Ch. 1 (structure and bonding), 2 (the nature of organic molecules) and Ch. 3 (the nature of organic reactions)

Wk 21:  Introduction and history of chemical synthesis, chemical space, medicinal chemistry, natural products and combinatorial chemistry; Hand in your take-home exam for FL

Wk 22: Advanced mechanistic chemistry + pick your research topic related to CombiChem

Wk 23: Combinatorial Chemistry and Diversity Orientated Synthesis + prepare for your presentation

Wk 24: Oral Presentation on CombiChem

Wk 25: Hand in your CombiChem essay

Week 10-13 NP

This section of the course will provide an overview of the modifications that occur to a protein between the translation of a gene and the functional gene product. These "post-translational modifications" will be related to the functional groups you learn about in CBMS103 and the mechanisms of functional group transformations. For example, serine phosphorylation can be related to reaction of acid anhydrides (or esters) with alcohols, ATP being a phosphoric acid anhydride or "phosphodiester". Alkylation with SAM can be related to the reaction of alkyl-halides (eg MeI, which you learnt about from a chemical perspective in Ch 7 and Ch 8 and Ch 12). Acetylation with acetylCoA can be related to esterification (Ch 10) and amide bond formation (Ch 12). Emphasis will be on sugar chemistry (see Blackman, Ch22; McMurry Ch14 & 15), the addition of the many types of different carbohydrate structures to the proteins, and how their chemical properties modify the behaviour of the protein.

Wk 25: Discussion of the known modifications that occur to proteins and how their chemical properties may affect the behaviour, structure and localisation of the proteins. (plus hand in essay for PK)

Wk 26: Introduction to the types of oligosaccharide modifications that are found on proteins, with examples of the many different isomeric sugar structures found. Choice of a particular glycoprotein to review.

Wk 27: Exploration of the methods used to characterise glycoproteins and the basis behind the methods used.

Wk 28: Oral (10 min. + 5 min for questions)

Wk 29: study break and hand in written report for NP (2 pages max)

Wk 30: Examination week (CBMS188 has no final exam)

CBMS188 is open to students outside the BAdvSc program, by permission and with an equivalent ATAR (>95) or with HD grade(s) in CBMS101, 102 and/or 103. CBMS188 is structurally the same as last year.  CBMS102 and CBMS103 are co-requisites for this unit.