No Lecture. Download unit guide, familiarise yourself with the curriculum and expectations and participate in virtual meeting on the CBMS188 web 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.
Wk 3: Discussion of the known modifications that occur to proteins and how their chemical properties may affect the behaviour, structure and localisation of the proteins.
Wk 4: 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. HAND IN ASSIGNMENT
Wk 5: Exploration of the methods used to characterise glycoproteins and the basis behind the methods used.
Wk 6: Oral presentations (10 min. + 5 min for questions)
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.
Wk 8: Review of basic stereochemistry, plus meso compounds
Wk 9 & 10: Methods for obtaining enantiopure compounds – separation from racemates, natural chiral pool, asymmetric synthesis
Wk 11: Measuring optical purity and less common forms of chirality (eg. allenes, atropisomers, phosphines, sulfoxides)
Wk 12: Workshop – student presentations on chirality problems
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.
Wk 2: 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'. Introduction to primary literature for researching your chosen biomacromolecule. Group Task - Plan your YouTube video for filming in week 10.
Wk 3: Group task– film your YouTube video in small groups
Wk 4: 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 5: Hand in your individual written report
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:
Wk 5: Localised and delocalised bonding: From Lewis to Schrödinger. Weak bonding interactions behind strong networks
Wk 6: Recognition motifs of the molecular world.
Wk 7: Time-dependent chemical complexity
Wk 8: hand in take-home exam
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)
Wk 8: Introduction and history of chemical synthesis, chemical space, medicinal chemistry, natural products and combinatorial chemistry. Complexity, complicatedness, cooperativity, multivalency and emergent properties
Wk 9: Combinatorial Chemistry and Diversity Orientated Synthesis + prepare for your presentation
Wk 10: Oral Presentation on CombiChem
Wk 11: Hand in your CombiChem essay
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.
Wk 11: 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 12: 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 final exam)