Students
CBMS188 – Advanced Chemistry I
2014 – FY1 Day
General Information
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| Unit convenor and teaching staff |
Unit convenor and teaching staff
Unit Convenor
Peter Karuso
Contact via peter.karuso@mq.edu.au
F7B232
any time ... for you guys
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| Credit points |
Credit points
3
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| Prerequisites |
Prerequisites
Admission to BAdvSc
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| Corequisites |
Corequisites
CBMS102 and CBMS103
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| Co-badged status |
Co-badged status
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| Unit description |
Unit description
This unit is a full-year unit based on contemporary topics in chemistry and biomolecular sciences. It is comprised of weekly research-focussed seminars and discussions. This unit caters for advanced students who are strong in chemistry and/or science and who are interested in pursuing a scientific career. It aims to encourage well-qualified students to reach their full potential. This unit is an extension of CBMS102 General Chemistry and CBMS103 Organic and Biological Chemistry. The unit will treat some topics in more depth and introduce others that are not covered in the regular undergraduate units. The weekly one-hour discussion sessions will also address recent advances in the molecular sciences. Student discussions are led by research scientists of the Department of Chemistry and Biomolecular Sciences and each student is mentored by a third year advanced chemistry student. In addition, students are encouraged to participate in the research activities of the department over the summer recess through vacation scholarships.
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Important Academic Dates
Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
Learning Outcomes
On successful completion of this unit, you will be able to:
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
- understand the chemistry, thermodynamics and kinetics that drives protein folding, the physical techniques involved in protein structure determination and the role of small molecules in probing biological systems
- understand the advantages and disadvantages of theoretical models of bonding, structure and intermolecular forces and how these control reactivity
- be able to compare and contrast the different types of combinatorial chemistry and how these relate to chemical diversity, natural products and the creation of new matter
- be able to draw and assign the stereochemistry of 8 monosaccharides and relate the biosynthesis of post-translational modifications to chemical reactions and functional groups and describe the limits to the heterogeneity found in oligosaccharide structures
- have the capability to use the chemical database Scifinder Scholar to retrieve information on specific chemicals, find methods for the synthesis of specific chemicals and find literature on chemistry
Assessment Tasks
| Name | Weighting | Due |
|---|---|---|
| module 1 | 17% | week 6 |
| Module 2 | 17% | week 10 |
| module 3 | 16% | Week 14 |
| module 4 | 17% | week 20 |
| module 5 | 17% | week 25 |
| module 6 | 16% | week 29 |
module 1
Due: week 6
Weighting: 17%
Production of a slowmation feature on crystal garden growth
On successful completion you will be able to:
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
Module 2
Due: week 10
Weighting: 17%
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 written lab report.
On successful completion you will be able to:
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
module 3
Due: Week 14
Weighting: 16%
Pick a macromolecule and make a group video on the role and structure of the macromolecule. In addition write an individual report on your macromolecule.
On successful completion you will be able to:
- understand the chemistry, thermodynamics and kinetics that drives protein folding, the physical techniques involved in protein structure determination and the role of small molecules in probing biological systems
module 4
Due: week 20
Weighting: 17%
takehome exame of structure and bonding
On successful completion you will be able to:
- understand the advantages and disadvantages of theoretical models of bonding, structure and intermolecular forces and how these control reactivity
module 5
Due: week 25
Weighting: 17%
You will make an oral presentation (PowerPoint; 3 slides) and then hand in a 2000 word essay on some aspect of combinatorial chemistry you find fascinating/intreaguing/interesting
On successful completion you will be able to:
- be able to compare and contrast the different types of combinatorial chemistry and how these relate to chemical diversity, natural products and the creation of new matter
module 6
Due: week 29
Weighting: 16%
assignment on the chemistry of post-translational modifications.
On successful completion you will be able to:
- be able to draw and assign the stereochemistry of 8 monosaccharides and relate the biosynthesis of post-translational modifications to chemical reactions and functional groups and describe the limits to the heterogeneity found in oligosaccharide structures
Delivery and Resources
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.
What has Changed?
The order of modules in S1 hase been changed
Unit Schedule
Wk 1:No Lecture. Download unit guide, familarise yourself with the curriculum and expectations and participate in virtual meeting on the CBMS188 web site.
Wk 2-5 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 (co-requiste) 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 Blackman 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 2: Introductory remarks and overview of the unit. Introduction to precipitation in the lab and in the field
Wk 3: Crystal gardens growth and colour
Wk 4: Crystal gardens growth and colour
Wk 5: Presentation of your slomation feature
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 setion build on Blackman Ch 12 and involves some thoery 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
Wk 7: Laboratory work
Wk 8: Discussion of results
Wk 9: Oral presentation and hand in lab report
Wk 10-13 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 10: 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 11: Introduction to primary literature for researching your chosen biomacromolecule. Group Task - Plan your YouTube video for filming in week 12.
Wk 12: Group task– film your YouTube video in small groups
Wk 13: 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 14: Hand in your individual written report
Wk 15: Examination week (CBMS188 has no mid-year exam)
Semester 2
Wk 16: introduction to SciFinder Scholar by your 3rd year mentors
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 extenstion 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 + hand in take-home exam in Wk 21
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
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: Group talks and final summaries and hand in your report in Wk 25.
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 many additions to the amino acid backbone go some way to explaining how ~25,000 genes can make more than a million proteins. Emphasis will be on sugar structures, 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.
Wk 26: Introduction to the types of oligosccharide 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) and draft written report
Wk 29: Hand in Written report (2 page maximum) on your chosen glycoprotein.
Wk 30: Examination week (CBMS188 has no final exam)
Learning and Teaching Activities
lectures
workshop
videos
presentation
assignments
web page
Policies and Procedures
Macquarie University policies and procedures are accessible from Policy Central. Students should be aware of the following policies in particular with regard to Learning and Teaching:
Academic Honesty Policy http://mq.edu.au/policy/docs/academic_honesty/policy.html
Assessment Policy http://mq.edu.au/policy/docs/assessment/policy.html
Grading Policy http://mq.edu.au/policy/docs/grading/policy.html
Grade Appeal Policy http://mq.edu.au/policy/docs/gradeappeal/policy.html
Grievance Management Policy http://mq.edu.au/policy/docs/grievance_management/policy.html
Disruption to Studies Policy http://www.mq.edu.au/policy/docs/disruption_studies/policy.html The Disruption to Studies Policy is effective from March 3 2014 and replaces the Special Consideration Policy.
In addition, a number of other policies can be found in the Learning and Teaching Category of Policy Central.
Student Code of Conduct
Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/support/student_conduct/
Student Support
Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/
Learning Skills
Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to improve your marks and take control of your study.
Student Services and Support
Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.
Student Enquiries
For all student enquiries, visit Student Connect at ask.mq.edu.au
IT Help
For help with University computer systems and technology, visit http://informatics.mq.edu.au/help/.
When using the University's IT, you must adhere to the Acceptable Use Policy. The policy applies to all who connect to the MQ network including students.
Graduate Capabilities
Capable of Professional and Personal Judgement and Initiative
We want our graduates to have emotional intelligence and sound interpersonal skills and to demonstrate discernment and common sense in their professional and personal judgement. They will exercise initiative as needed. They will be capable of risk assessment, and be able to handle ambiguity and complexity, enabling them to be adaptable in diverse and changing environments.
This graduate capability is supported by:
Learning and teaching activities
- write 2 essays and one takehome exam
Commitment to Continuous Learning
Our graduates will have enquiring minds and a literate curiosity which will lead them to pursue knowledge for its own sake. They will continue to pursue learning in their careers and as they participate in the world. They will be capable of reflecting on their experiences and relationships with others and the environment, learning from them, and growing - personally, professionally and socially.
This graduate capability is supported by:
Learning outcomes
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
- understand the chemistry, thermodynamics and kinetics that drives protein folding, the physical techniques involved in protein structure determination and the role of small molecules in probing biological systems
- understand the advantages and disadvantages of theoretical models of bonding, structure and intermolecular forces and how these control reactivity
- be able to compare and contrast the different types of combinatorial chemistry and how these relate to chemical diversity, natural products and the creation of new matter
- be able to draw and assign the stereochemistry of 8 monosaccharides and relate the biosynthesis of post-translational modifications to chemical reactions and functional groups and describe the limits to the heterogeneity found in oligosaccharide structures
Learning and teaching activities
- write 2 essays and one takehome exam
Discipline Specific Knowledge and Skills
Our graduates will take with them the intellectual development, depth and breadth of knowledge, scholarly understanding, and specific subject content in their chosen fields to make them competent and confident in their subject or profession. They will be able to demonstrate, where relevant, professional technical competence and meet professional standards. They will be able to articulate the structure of knowledge of their discipline, be able to adapt discipline-specific knowledge to novel situations, and be able to contribute from their discipline to inter-disciplinary solutions to problems.
This graduate capability is supported by:
Learning outcomes
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
- understand the chemistry, thermodynamics and kinetics that drives protein folding, the physical techniques involved in protein structure determination and the role of small molecules in probing biological systems
- understand the advantages and disadvantages of theoretical models of bonding, structure and intermolecular forces and how these control reactivity
- be able to draw and assign the stereochemistry of 8 monosaccharides and relate the biosynthesis of post-translational modifications to chemical reactions and functional groups and describe the limits to the heterogeneity found in oligosaccharide structures
- have the capability to use the chemical database Scifinder Scholar to retrieve information on specific chemicals, find methods for the synthesis of specific chemicals and find literature on chemistry
Learning and teaching activities
- 24 lectures
- write 2 essays and one takehome exam
Critical, Analytical and Integrative Thinking
We want our graduates to be capable of reasoning, questioning and analysing, and to integrate and synthesise learning and knowledge from a range of sources and environments; to be able to critique constraints, assumptions and limitations; to be able to think independently and systemically in relation to scholarly activity, in the workplace, and in the world. We want them to have a level of scientific and information technology literacy.
This graduate capability is supported by:
Learning outcomes
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
- understand the advantages and disadvantages of theoretical models of bonding, structure and intermolecular forces and how these control reactivity
- be able to compare and contrast the different types of combinatorial chemistry and how these relate to chemical diversity, natural products and the creation of new matter
Learning and teaching activities
- deliver 3 presentation with powerpoint
- write 2 essays and one takehome exam
Problem Solving and Research Capability
Our graduates should be capable of researching; of analysing, and interpreting and assessing data and information in various forms; of drawing connections across fields of knowledge; and they should be able to relate their knowledge to complex situations at work or in the world, in order to diagnose and solve problems. We want them to have the confidence to take the initiative in doing so, within an awareness of their own limitations.
This graduate capability is supported by:
Learning outcomes
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
- describe the fundamental principles of electrochemistry and apply electrochemistry to simple chemical analysis, clinical diagnostics and environmental detection
Learning and teaching activities
- learn how to use SciFinder Scholar
- write 2 essays and one takehome exam
Creative and Innovative
Our graduates will also be capable of creative thinking and of creating knowledge. They will be imaginative and open to experience and capable of innovation at work and in the community. We want them to be engaged in applying their critical, creative thinking.
This graduate capability is supported by:
Learning outcome
- relate "crystal garden" growth to the chemical processes of precipitation, diffusion and osmosis, molecular electronic configurations
Learning and teaching activities
- shoot 1 video for youtube
- write 2 essays and one takehome exam
Effective Communication
We want to develop in our students the ability to communicate and convey their views in forms effective with different audiences. We want our graduates to take with them the capability to read, listen, question, gather and evaluate information resources in a variety of formats, assess, write clearly, speak effectively, and to use visual communication and communication technologies as appropriate.
This graduate capability is supported by:
Learning outcomes
- understand the chemistry, thermodynamics and kinetics that drives protein folding, the physical techniques involved in protein structure determination and the role of small molecules in probing biological systems
- be able to compare and contrast the different types of combinatorial chemistry and how these relate to chemical diversity, natural products and the creation of new matter
- be able to draw and assign the stereochemistry of 8 monosaccharides and relate the biosynthesis of post-translational modifications to chemical reactions and functional groups and describe the limits to the heterogeneity found in oligosaccharide structures
Learning and teaching activities
- deliver 3 presentation with powerpoint
- write 2 essays and one takehome exam