Summer vacation (Dec-Feb)
4 weeks full-time (minimum 40 h/week) lab attachment to carry out closely supervised real research.
Write up your results in the form of a scholarly article (journal) using a template of your/supervisor's choice - write-up dues before Easter
No Lecture. Download unit guide, familiarise yourself with the curriculum and mentoring expectations and participate in virtual meeting on the CBMS389/288 iLearn site.
Week 2 PK
Introductions, background and unit organisation.
Week 3-6 MA
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 CBMS107 and the mechanisms of functional group transformations. For example, serine phosphorylation can be related to reaction of acid anhydrides (or esters) with alcohols (see McMurry Ch 10), ATP being a phosphoric acid anhydride (McMurry Ch 10, 17) 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 CBMS107 (McMurry, Ch 7). Acetylation with acetylCoA can be related to esterification and amide bond formation (McMurry Ch 10, 15). Emphasis will be on sugar chemistry (McMurry Ch 14), the addition of the many types of different carbohydrate structures to the proteins, and how their chemical properties modify the behaviour of the protein.
You will be expected to mentor 2 CBMS188 students in this topic
Week 8-12 JJ
In this section, we will firstly provide an overview of the concept of stereochemistry as presented in CBMS107 (McMurry Ch 6). We will then extend this, with a particular focus on chirality. This will include exploring methods to obtain enantiopure molecules, and less common forms of chirality, such as molecules with no chiral carbon or containing heteroatoms as the chiral centre.
You will be expected to lead the workshops of stereochemistry for the CBMS188 students
Wk 1: introduction to SciFinder Scholar by your 3rd year mentors (in 200/300-level chem labs)
Wk 2-4 LB
This three-week section (6 lectures) 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.
You will be expected to mentor the CBMS188 students in making a video of their pet protein
Week 5-7 FL
his 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 parts of CBMS107 and CBMS108 as it deals with more advanced theories on bonding, structures, conformations, noncovalent interactions, and reaction energy control. These are extensions of structure and bonding, shape of organic molecules, and nature of organic molecules/reactions. Specific topics include:
You will be expected to mentor CBMS188 students who have not managed to get the the required level
Week 8-10 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)
You will be expected to mentor the CBMS188 students on their choice of topic
Wk 11-13 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.
You will be expected to mentor the CBMS188 studetns and help them understand crystal gardens and make a video/web page.