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Foundation Chemistry for Biochemists II - CHE00009C

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  • Department: Chemistry
  • Module co-ordinator: Dr. Seishi Shimizu
  • Credit value: 30 credits
  • Credit level: C
  • Academic year of delivery: 2022-23
    • See module specification for other years: 2021-22

Module summary

This module contains lecture courses of fundamental importance in organic, inorganic and physical chemistry. These lecture courses are supported by tutorial sessions (for which written work is set) as well as workshops. The module also carries practical courses in basic chemistry and synthetic chemistry.

Together with the Autumn Term module Foundation Chemistry for Biochemists I, this Spring / Summer Term module aims to provide the Biochemistry student with a firm foundation in chemistry. The emphasis in this course is on the principles of Physical and Organic Chemistry, as well as Analytical. The course forms a prerequisite for the subsequent chemistry modules specifically designed for Biochemistry students. Collectively, these modules equip the Biochemistry student for courses that survey the physical properties and interactions of biological macromolecules such as proteins and DNA.

Module will run

Occurrence Teaching period
A Spring Term 2022-23 to Summer Term 2022-23

Module aims

Together with the Autumn Term module Foundation Chemistry for Biochemists I, this Spring / Summer Term module aims to provide the Biochemistry student with a firm foundation in chemistry. The emphasis in this course is on the principles of Physical, Organic and Inorganic Chemistry.The course forms a prerequisite for the subsequent chemistry modules specifically designed for Biochemistry students. Collectively, these modules equip the Biochemistry student for courses that survey the physical properties and interactions of biological macromolecules such as proteins and DNA.

Module learning outcomes

This term will introduce key foundation themes of organic, inorganic, physical and analytical chemistry, with practical courses complementing the lectures. This terms work provides a vital foundation for the rest of the biochemistry degree.

Appreciation of basic chemical concepts in:

  • Basics of transition metal chemistry
  • Fundamentals 2nd law thermodynamics and applications to electrochemistry
  • Basic laws of kinetics
  • Substitution and elimination in organic reactions
  • Structures and reactions of alkenes and alkynes
  • Structures and reactions of organic carbonyls
  • Fundamentals of aromatic chemistry
  • Molecular orbital theory

Practical chemistry skills:

  • Continued development of practical skills, following on from CHE00008C

Computational skills:

  • Molecular graphics and protein databank skills

Module content

Molecular Orbital Theory

CED

5 lectures +1h tutorial

The principles of MO theory based upon wave functions.

The application of MO theory to diatomic molecules.

Second Law/electrochemistry

PBK/AP

6 lectures + 2h central workshop (PBK)/4 lectures + workshop (AP)

The Second Law of Thermodynamics

Application to reactions. applied to reactions

The concepts of entropy and free energy.

Transition Metals

AKDK

10 lectures + 1h tutorial

The first transition series Sc to Cu.

The origin of colour and magnetic properties in terms of the filling of d orbitals

The role of transition metals on catalysis.

Kinetics

MJE & MSS

10 lectures + 1h tutorial

The methods of determining rates of reaction, effects of concentration and temperature on the rates of reaction.

Application to the understanding of reaction mechanisms.

Haloalkanes, Alkenes & Alkynes

ASM

9 lectures + 1h tutorial

Understanding reaction mechanism as a means of rationalising the stereoselectivity and regioselectivity observable in the reactions of hydrocarbons.

Electrophilic, nucleophilic and radical addition reactions of alkenes and alkynes and Markovnikov and anti-Markovnikov regioselectivity in the addition of hydrogen halides.

Aromatics and Organic Carbonyls

GAH

8 lectures + 1h tutorial

The 'special properties' of benzene and related cyclic compounds and ions with (4n + 2)-electrons.

The mechanistic interpretation involving the intermediate carbenium ion accounts for relative reactivities and regioselectivity of attack.

The structure and reactions involving the carbonyl groups.

Practical Chemistry (Spring/Summer)

SKF & DSP

Spr/Sum lab sessions

Students will undertake a number of practicals which build on skills introduced during the autumn term, and encounter new techniques to further develop their practical skills.

Molecular Graphics & Protein Data Bank Workshop (Summer) KDC 1 x 3h workshop

Students will use free-access graphics programmes for display and manipulation of protein/DNA structures. They will perform practical analysis of secondary, tertiary and quaternary structures, 3-D analysis of selected enzyme mechanisms and learn the basics of making figures of proteins for presentations and written work.

Assessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed Exam		 2 hours 70
Essay/coursework
Assessed Workshop : Aromatics and Organic Carbonyls		 0.5 hours 10
Essay/coursework
Practical work portfolio		 N/A 10
Online Exam -less than 24hrs (Centrally scheduled)
Online assessment : Practical online assessment		 1 hours 10

Special assessment rules

Non-reassessable

Additional assessment information

The assessment of the module will consist of an exam paper (70 %), assessments related to the practical sessions (20 % over Spring and Summer terms), and aromatics and organic carbonyls assessed workshop (10 %).

Reassessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed Exam		 2 hours 70
Online Exam -less than 24hrs (Centrally scheduled)
Online assessment : Practical online assessment		 1 hours 10

Module feedback

  • Tutorials/workshops: Written feedback will be given for tutorial work within a week. Written and/or oral feedback for workshops will be given either during the sessions or within a week.

  • Summative Workshop: Aromatics/Carbonyl assessed
    workshop will take place on Friday, Week 4,, Summer Term.

  • Practicals: feedback will be provided on all summative practical work within 20 working days.

  • Exams: Closed exam results with per-question breakdown are returned to the students via supervisors within 5 weeks (as per special approval by the University Teaching Committee). Outline answers are made available via the Chemistry web pages when the students receive their marks, so that they can assess their own detailed progress/achievement. The examiners’ reports for each question are made available to the students via the Chemistry web pages.

Indicative reading

Burrows, Holman, Parsons, Pilling and Price: Chemistry3 (Oxford University Press)


The information on this page is indicative of the module that is currently on offer. The University is constantly exploring ways to enhance and improve its degree programmes and therefore reserves the right to make variations to the content and method of delivery of modules, and to discontinue modules, if such action is reasonably considered to be necessary by the University. Where appropriate, the University will notify and consult with affected students in advance about any changes that are required in line with the University's policy on the Approval of Modifications to Existing Taught Programmes of Study.