CHEM1603: Chemistry For Biologists

Course Organizer: Prof A Sella (email:chem160x@ucl.ac.uk)

Lecturers: Dr C Blackman, Dr D Caruana, Prof J R G Evans, Dr S Howorka, Dr K Holt, Prof P F McMillan, and Prof A Sella

Normal prerequisite: A-level Chemistry or equivalent

Units: 1 unit

Facebook: https://www.facebook.com/groups/78989194110/

Twiter feed: #UCLChem160x

Moodle: https://moodle.ucl.ac.uk/course/view.php?id=4979

Aims

The aim of this course is to provide students with the key foundations in chemistry needed to develop an understanding of biological systems at a molecular level. The course has a good balance of physical and organic chemistry. Life Science students expecting to take higher level courses in chemistry, biochemistry/molecular biology, pharmacology or neuroscience should take this course. It is highly recommended for other Life Science students

This course is the normal pre-requisite for CHEM2302

Objectives

  • to understand the structure and bonding in simple molecules
  • to understand the basic principles of membrane self-assembly
  • to use infrared and NMR spectroscopy to identify simple organic molecules
  • to understand pH and its measurement
  • to understand equilibrium and the factors which determine it (enthalpy entropy and the Gibbs energy)
  • to formulate and to understand the factors influencing the rates of chemical reactions
  • to know key transformations of major organic functional groups
  • to be familiar with key biological macromolecules, their structure and chemistry
  • to understand the role played by metal ions in biological systems.

Course Structure

  • Lectures: 40
  • Tutorials: 0
  • Workshops: 12
  • Labs: 6

Assessment

  • Exam: 60% (3 hours normally held in May)
  • Lab: 20% (in class assessment and two open book online tests)
  • Coursework: 20% (3 online Tests)

Practical course organizer:

Recommended Texts

  • Burgess Holman Parsons et a. "Chemistry3", Oxford Press with additional resources in a custom bundle from Waterstones, Gower Street.

This custom bundle of resources will be only be available available from Waterstones Gower Street.

Second hand books of previous years' texts may also be available - look at bulletin boards round college. However, note that the recommended text has been changed twice in the past two years in response to critical comment from students in course evaluations.

Further Reading

  • Any General Chemistry text. Browse around in the library to see what is available and get a second or a third opinion.

Reading for Rainy Days

  • P Levi, "The Periodic Table", Abacus Books
  • B Selinger, "Chemistry in the Marketplace" Harcourt Brace
  • P Ball, "H2O The Biography of Water"
  • P Ball, "Nature's Patterns: A Tapestry in Three Parts" Oxford UP 2009 (3 vols. Shapes, Flow, Branches)
  • H McGee, "On Food and Cooking - Science and Lore of the Kitchen", Prentice Hall, 1997

Course Outline

The course is divided into a series of eight 5-lecture blocks, each of which includes revision sections either as a separate session or embedded into the course. A set of 5 additional workshops in"Applicable Mathematics" is included for those students without an A-Level in the subject.

There will be an Introductory Lecture on the Thursday of Induction week at 9 am in the Chemistry Auditorium

The course has an associated Moodle Headquarters (requires enrolment key)

A: Structure, Bonding, and Self-Assembly of Biological Structures (Holt)

  • Electron configuration of atoms, Pauli principle, Hund's rule. Covalent bonding in simple molecules - principally made up of C, O, H, N, S, P - using electron-sharing arguments (Lewis structures). Single and multiple bonds, and bond order.
  • Geometry of covalently bonded molecules based on valence shell electron pair repulsion (VSEPR). Orbital overlap and hybridisation models for bonding (Valence Bond Theory). Sigma and pi bonds, rationalized using diagrams for orbital overlap.
  • Basic Molecular Orbital Theory, as an alternative representation of bonding in molecules. Electronegativity, and its relation to bond polarity, and ionic vs. covalent bonding.
  • The role of non-covalent interactions between molecules in determining the properties of condensed-phase and biological materials. The interaction between charges, dipoles, and induced dipoles in varying combinations. How molecular liquids behave as solvents, in particular their differing polarity.
  • The properties of water as nature's solvent, in particular the dissociation and hydration of ionic species in water. The hydrogen bonding within bulk water, between water and solute molecules, and within and between other molecules. The origin of hydrophobic interactions which cause the aggregation of non-polar moieties in water. Solvation of non-polar molecules.
  • The concept of self-assembly, building from the non-covalent interactions studied previously. Examples to include: self-assembly of lipids into membranes, protein folding, membrane proteins, viruses, cytoskeleton, liposomes.

B: Seeing Biomolecules - Spectroscopy and Quantification (McMillan)

  • The nature of light and how it interacts with molecules
  • Vibrations of molecules : basic theory
  • Infrared (IR) spectroscopy of organic molecules and functional groups
  • UV-visible spectroscopy and electronic structure
  • Atomic and molecular orbitals and energy levels : a review
  • UV-vis spectra of organic molecules and species
  • Nuclear Magnetic Resonance (NMR) spectroscopy : basic concepts
  • Proton (1H) NMR spectra : shielding and chemical shifts
  • High resolution 1H NMR spectra : coupling patterns
  • Interpreting NMR spectra of organic molecule

C: Chemical Equilibrium and Chemical Thermodynamics (Sella)

  • Definition of energy, kinds of energy, units,
  • Energy consumption and power output - comparisons across different organisms
  • The First Law - Conservation of Energy
  • Heat and Work as mechanisms of energy transfer - Temperature difference as the driver of heat.
  • The Second Law - The Quality of Energy
  • Spontaneous vs Irreversible change - Free Energy as a criterion.
  • The idea of deltaG ATP as fundamental biological energy unit.
  • Simple introduction to Boltzmann's ideas
  • Excursion into energy flows. Dissipative structures or Protein Folding

D: Concentrations, pH and Equilibria (Caruana)

  • Revision of acids and bases. Strong and weak acids. Multiple ionisation.
  • Buffers. Buffering capacity.
  • Titration curves. Indicators.
  • Revision of electrochemistry. Galvanic cells.
  • Standard potentials and Free Energy.
  • Chemical potential and extent of reaction.
  • Equilibria in redox reactions.
  • The Nernst equation. Application of the Nernst equation.
  • Membrane potentials.
  • Reference electrodes and applications in biology.

E: The Speed of Life - Chemical and Biological Kinetics (Sella)

  • Nature and scope of kinetics.
  • Meaning and definition of rate of reaction.
  • Factors influencing rate of reaction.
  • Concept of order of reaction. Examples of reactions with simple orders. Pseudo-order reactions. Order and stoicheiometry. Integrated rate equations for first and second order processes.
  • Experimental methods in kinetics. Determination of reaction order and rate coefficients. Kinetics and reaction mechanism. Concepts of elementary processes and molecularity. The steady state approximation.
  • Enzyme kinetics as an example of the application of the steady state approximation. The Michaelis-Menten equation for reactions involving one intermediate.
  • Effect of temperature on reaction rate - the Arrhenius equation. Theories of reaction rates: collision theory and transition state theory. Catalysts.
  • An excursion into biological pattern formation.

F: The Bricks of Biological Architecture - Functional Groups and Reactivity (Howorka)

Preparations and transformations of functional groups of relevance to biological applications, e.g.:

  • Oxidation and reduction
  • Substitution reactions
  • Addition reactions
  • Elimination reactions
  • Formation of ethers, acetals and aldols

G: The Wheels and Spokes of Life- Biological Macromolecules (Howorka)
Discussion of the structures and properties of the following classes of molecules and associated techniques:

  • Amides
  • Amino acids
  • Peptide bond formation
  • Electrophoresis
  • Proteins

H: The Inorganic Chemistry of Life (Blackman)

  • The Periodic Table and the elements of life
  • Metal ions - hard and soft - polarizability and polarizing power
  • Ligands and how they bind to metals
  • Factors affecting binding strength - the stability constant
  • Metal binding sites - selectivity
  • The role of metal ions in biological systems - examples drawn from iron chemistry - hydrogenase, ferredoxin, haem proteins etc.

X: Applicable Mathematics (JRGE), 5 workshops

This section provides five hours of tuition and tutor-guided, in-class problem solving and is aimed at students who have Mathematics to GCSE. The aim is to rekindle an interest in maths by providing confidence in simple operations at first and then to introduce elementary calculus. The content will include: manipulation of fractions, expansion of brackets, quadratic equations, rearranging equations, indices, fractional indices, logarithms, pH, simultaneous equations, combinations and permutations, the straight line y = mx + c, differentiation and integration. As well as the in-class problem solving, a substantial body of Moodle-based exercises has been provided. In order to take advantage of this section of CHEM160X, given the limited contact hours, it is essential that students adopt a radically different learning strategy based on extensive practice at problem solving.

Applicable Maths material will be examined during tests.