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CBMS188 – Advanced Chemistry I

2017 – 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
Lecturer
Louise Brown
Contact via e-mail
E8C305
Tuesday-Friday only
Lecturer
Joanne Jamie
F7B231
anytime
Lecturer
Morten Andersen
Contact via 7487
F7B306
anytime
Lecture
Fei Liu
Contact via 8312
F7B330
make an appointment
Lecturer
Ian Jamie
any time
Credit points Credit points
3
Prerequisites Prerequisites
Admission to BAdvSc
Corequisites Corequisites
(CBMS102 or CBMS108) and (CBMS103 or CBMS107)
Co-badged status Co-badged status
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 CBMS107 and CBMS108. 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, all students are encouraged to participate in the research activities of the department over the summer recess through vacation scholarships.

Important Academic Dates

Information about important academic dates including deadlines for withdrawing from units are available at http://students.mq.edu.au/student_admin/enrolmentguide/academicdates/

Learning Outcomes

  1. 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
  2. be able to identify chiral and achiral molecules including those with multiple stereocentres, describe methods for obtaining enantiopure compounds and determine the optical purity of compounds given specific optical rotations or enantiomeric excess values.
  3. 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
  4. understand theoretical models of bonding and how these control structure and reactivity
  5. 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
  6. 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
  7. You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

General Assessment Information

Assessment is based on assignments/workshops (total of 6 major topics), a take home exam (1), essays (2), and short orals (2 group presentation).  These assessment tasks are provided so that you will have the opportunity to use the information gained in the discussion session to test your degree of understanding of those topics and to gain discipline specific knowledge and skills as well as develop your graduate capabilities attributes. There is no final exam for this unit.

A satisfactory/unsatisfactory grade is obtained overall.  You must perform satisfactorily in all parts of the assessment to achieve an overall satisfactory mark.  Assignments will be marked with a A/B/C/D/F or similar marking scheme and you are encouraged to perform at the best of your abilities.  A high standard of performance is expected and higher marks will allow entry into summer vacation scholarships.  An unsatisfactory grade will result from a student not submitting all assignment tasks or showing a partial, superficial or faulty understanding of the topics.

Please note that CBMS107 and CBMS108 are co-requisites for this unit (unless you have done CBMS102 and CBMS103 previously)

Assessment Tasks

Name Weighting Hurdle Due
module 1 16% week 3 and week 5
module 2 17% week 12
module 3 16% S2; Weeks 3 and 4
module 4 17% S2; Week 7
module 5 17% S2; week 10 and 11
module 6 17% S2; week 13

module 1

Due: week 3 and week 5
Weighting: 16%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

assignment on the chemistry of protein post-translational modifications (40%)

group (2) presentation on you assigned post-translational modification (60%)


This Assessment Task relates to the following Learning Outcomes:
  • 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

module 2

Due: week 12
Weighting: 17%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

This will be a workshop assignment, mentored by the CBMS389 students.


This Assessment Task relates to the following Learning Outcomes:
  • be able to identify chiral and achiral molecules including those with multiple stereocentres, describe methods for obtaining enantiopure compounds and determine the optical purity of compounds given specific optical rotations or enantiomeric excess values.

module 3

Due: S2; Weeks 3 and 4
Weighting: 16%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

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.


This Assessment Task relates to the following 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

module 4

Due: S2; Week 7
Weighting: 17%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

Take home exam on structure and bonding


This Assessment Task relates to the following Learning Outcomes:
  • 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
  • understand theoretical models of bonding and how these control structure and reactivity

module 5

Due: S2; week 10 and 11
Weighting: 17%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

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/intriguing/interesting


This Assessment Task relates to the following Learning Outcomes:
  • 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
  • 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: S2; week 13
Weighting: 17%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)

to be announced


This Assessment Task relates to the following Learning Outcomes:
  • You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

Delivery and Resources

No required text.  Background readings from co-requisite CBMS107 and CBMS108 may be required.

Lectures in Semester 1 will be Tuesday 9-10AM in W5A105

Unit Schedule

Semester 1

Week 1

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 7

No Lecture.

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

Week 13

no lecture

Semester 2

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)

Learning and Teaching Activities

lectures

34 lecture/discussion groups

workshop

learn how to use SciFinder Scholar

videos

shoot 1 video for YouTube

presentation

deliver 3 presentation with PowerPoint

assignments

write 3 essays and one take-home exam

web page

create one web page for crystal gardens

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_2016.html

Grade Appeal Policy http://mq.edu.au/policy/docs/gradeappeal/policy.html

Complaint Management Procedure for Students and Members of the Public http://www.mq.edu.au/policy/docs/complaint_management/procedure.html​

Disruption to Studies Policy (in effect until Dec 4th, 2017): http://www.mq.edu.au/policy/docs/disruption_studies/policy.html

Special Consideration Policy (in effect from Dec 4th, 2017): https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policies/special-consideration

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/

Results

Results shown in iLearn, or released directly by your Unit Convenor, are not confirmed as they are subject to final approval by the University. Once approved, final results will be sent to your student email address and will be made available in eStudent. For more information visit ask.mq.edu.au.

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 Enquiry Service

For all student enquiries, visit Student Connect at ask.mq.edu.au

Equity 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.

IT Help

For help with University computer systems and technology, visit http://www.mq.edu.au/about_us/offices_and_units/information_technology/help/

When using the University's IT, you must adhere to the Acceptable Use of IT Resources Policy. The policy applies to all who connect to the MQ network including students.

Graduate Capabilities

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

  • 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
  • be able to identify chiral and achiral molecules including those with multiple stereocentres, describe methods for obtaining enantiopure compounds and determine the optical purity of compounds given specific optical rotations or enantiomeric excess values.
  • 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
  • understand theoretical models of bonding and how these control structure and reactivity
  • 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
  • You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

Assessment tasks

  • module 1
  • module 2
  • module 3
  • module 4
  • module 6

Learning and teaching activities

  • 34 lecture/discussion groups
  • write 3 essays and one take-home 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:

Assessment tasks

  • module 2
  • module 4

Learning and teaching activities

  • learn how to use SciFinder Scholar
  • write 3 essays and one take-home 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

  • 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
  • understand theoretical models of bonding and how these control structure and 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
  • 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

Assessment tasks

  • module 3
  • module 4
  • module 5

Learning and teaching activities

  • 34 lecture/discussion groups
  • deliver 3 presentation with PowerPoint
  • write 3 essays and one take-home 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

  • be able to identify chiral and achiral molecules including those with multiple stereocentres, describe methods for obtaining enantiopure compounds and determine the optical purity of compounds given specific optical rotations or enantiomeric excess values.
  • understand theoretical models of bonding and how these control structure and 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
  • You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

Assessment tasks

  • module 2
  • module 4
  • module 5

Learning and teaching activities

  • deliver 3 presentation with PowerPoint
  • write 3 essays and one take-home 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 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
  • You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

Assessment tasks

  • module 3
  • module 6

Learning and teaching activities

  • shoot 1 video for YouTube
  • write 3 essays and one take-home exam
  • create one web page for crystal gardens

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

  • 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
  • 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
  • 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
  • You will be able to explain the chemical processes of precipitation, diffusion and osmosis as relating to "crystal gardens", and the origin of colour in transition metal salts, at an introductory level

Assessment tasks

  • module 1
  • module 3
  • module 5
  • module 6

Learning and teaching activities

  • shoot 1 video for YouTube
  • deliver 3 presentation with PowerPoint
  • write 3 essays and one take-home exam
  • create one web page for crystal gardens

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 3 essays and one take-home exam

Changes from Previous Offering

CBMS188 has been completely redesigned for 2017.  Changes include the running of 2 modules in S1 and 4 modules in S2.  Students are advised to do only 3 other subjects in S2 and 4 other subjects in S1. CBMS107 and CBMS108 are co-requisites of CBMS188 UNLESS you have done CBMS102 and CBMS103 last year.

CBMS188 is required for the BAdvSc program, by permission and with an equivalent ATAR (>97) or with HD/D grade(s) in both CBMS102 and 103. CBMS188.