Download BIO00004C Molecular biology and biochemistry (PDF , 72kb)

MODULE:
Molecular Biology & Biochemistry
MODULE NUMBER:
BIO00004C
JACS CODE:
C700
STAGE/YEAR:
1
CREDITS:
20
ORGANISER:
Dr Set Chong
SUBJECT COMMITTEE:
Biochemistry
VERSION:
12 Nov 2015
TERMS TAUGHT:
Au,Sp,Su 2016/17
PREREQUISITES:
Students should have met the admissions standards required by the
Department of Biology for enrolment on the course.
RECOMMENDATIONS:
AIMS
This module deals with the structure and function of fundamental chemical molecules of a cell. It starts with an overview of the module and advanced applications that
depend on the subjects covered in the module. It then covers the basic chemical building blocks of cells, from elements to macromolecules. The structure of nucleic
acids will be introduced, and its importance to the mechanism of DNA replication. Then, the different levels of protein structure will be defined and protein-protein
interactions, covalent modification and the nature of membrane proteins, described. The functionality of proteins as enzymes will be discussed in detail. Following an
introduction to lipid and carbohydrate structures, the role of the various macromolecules in the context of membrane flow, cell shape, etc. will be discussed. Energy
and metabolism is introduced by discussing the important concept of free energy and relating this to the central role of ATP and coupling of biochemical processes.
The course then surveys carbohydrate and fat metabolism, photosynthesis and related metabolic processes in plants, and concludes with section on the integration of
metabolism.
LEARNING OUTCOMES:
1. To be able to describe the main chemical components of cells, their structural properties, how these relate to their functions, and how they are altered during cellular
processes
2. To be able to describe and explain how covalent and non-covalent interactions bring about the assembly of cellular components and macromolecules
3. To be able to explain theoretical frameworks (such a Michaelis Menten kinetics, the laws of thermodynamics and the chemiosmotic theory) that allow us to
understand function of biological molecules and cells
4. To be able to integrate knowledge about heterotrophic metabolism (of carbohydrates & lipids) and phototrophic metabolism and how they relate to energy
metabolism via ATP
5. To be able to relate knowledge of biological molecules to health and disease and to their application in biotechnology
6. To be able to apply quantitative approaches to perform basic calculations related to acid-base chemistry, redox reactions, and to analyse and evaluate enzyme
kinetics data gathered in practical classes
SYNOPSIS OF TEACHING:
Event
Duration (Hrs)
Topic
Staff
Room type
Timing
Lecture 1
1
Introduction. Highlights in Molecular Biology and Biochemistry.
Peter McGlynn
L
Autumn term
Lectures 2 and 3
1,1
Chemical composition of living things. Acids and bases. That
macromolecules are made of building blocks. Covalent and noncovalent assemblages.
Set Chong
L
“
Lectures 4 and 5
1,1
Structural features of DNA and RNA.
Set Chong
L
“
Lectures 6,7,8,9,10
1,1,1,1,1
Proteins are the molecules that carry out active functions in the cell. Peter McGlynn
Roles of amino acids, and levels of organisation in the structure of
proteins (primary, secondary, tertiary, quaternary). Different types of
non-covalent interactions. Protein folding (and disease). Co-factors /
covalent modification.
L
“
Lectures 11,12
1,1
The enzyme in the cell, catalysis and specificity, active sites,
stereospecificity, flexibility, conformational changes, induced-fit.
Enzyme assays and enzyme kinetics. Classification of enzymes.
Moir
L
“
Lecture 13
1
Serine proteases: control, mechanism, specificity and evolutionary
relationships within an extensive enzyme family.
Moir
L
“
Lecture 14
1
Allosteric enzymes and the control of enzyme activity. Cooperativity Moir
and feedback inhibition, aspartate transcarbamylase as a case
study. Survey of other control mechanisms.
L
“
Lecture 15
1
Protein/enzyme engineering; methods for designing new and
modified enzymes, studies with subtilisin. Applications of enzymes
in biotechology.
Moir
L
“
Workshop
2hrs
Solving problems related to material taught in Autumn term
Split class to run (basic calculations, pH, etc.) See worksheet on the VLE. Each
student does one 2-hr workshop.
Moir, Peter McGlynn,
Workshop
Week 10
Practical /Lecture (1)
1
Set Chong
L – where tbc
Must be after
L10
Practical 1
Duration 3 hours, Separation of biomolecules by column chromatography
Set Chong
Where tbc
Must be after
L10 & Practical
L1
Lectures 16,17,18
1,1,1
Lipids, membrane bilayers. Carbohydrates: Monosacharides and
polysaccharides. Cell walls and extracellular matrix. Roles of lipids
and proteins in membrane function.
Baumann
L
Spring
Lecture 19
1
Introduction to energetics: free energy and the central role of ATP Maathuis
as energy currency. Redox potentials and their relationship to Gibbs
free energy.
L
“
Introduction to practicals[1]
Lectures 20,21,22, 23,24
1,1,1,1,1
Metabolism. Overview and concepts of metabolism; how cells utilize Ungar
different sugar nutrients, regulation of glycogen metabolism;
detailed discussion of glycolysis, the TCA cycle and the role of
fermentation; regulation of these pathways, how energy generation
is balanced with the efficient turnover of available nutrients; how
and why cells choose one pathway over another; generation of a
redox currency for biosynthetic use – the pentose phosphate
pathway; select examples of metabolic aspects of diseases.
L
“
Lectures 25, 26
1,1
( i) The cell: control of glycolysis, the glucose/fatty acid cycle and
fatty acid oxidation.
(ii) The tissue: examples of the specialisation of carbohydrate and
fat metabolism in various tissues.
(iii) The organism - whole body co-ordination of metabolism by
hormones: eg obesity and starvation
L
“
Lectures 27, 28
1,1
Conservation of free energy from carbohydrate catabolism as
Maathuis
NADH- quantitative assessment. The pathway of electrons from
NADH to oxygen: technical approaches; functions of the major
protein complexes; prosthetic groups in the electron-transporting
complexes. Coupling electron transport to ATP synthesis and
identification of those complexes involved in ATP synthesis.
Measurement of P:O ratios. How ATP is synthesised: chemiosmotic
coupling. Quantifying the energy in transmembrane solute
gradients. The protonmotive force in coupled mitochondria; proton
flows, stoichiometry and energetics. Proton flow and the
phenomenology of redox-phosphorylation coupling. Ubiquity of the
ATP synthase at “energy-coupling” membranes. Alternative uses or
the PMF in bacteria: solute uptake and swimming.
L
“
Lectures 29, 30, 31
1,1,1
Photosynthesis. Transduction of light energy in chloroplasts. The
Maathuis
nature of light. The energy in a photon. Comparison of light energy
with other forms of free energy. Pigments, absorption spectra and
excited states. “Light-harvesting” and resonance energy transfer;
antenna and reaction centre chlorophylls. Loss of energy in excited
reaction centres and generation of redox reactions. Serial
arrangement of photosystems I and II. Redox reactions and carbon
fixation in chloroplasts. The components of the redox chain. The
PSII reaction centre; cytochrome b6f complex; the PSI reaction
centre. Cyclic phosphorylation. Carbon fixation, the Calvin cycle and
pathways of starch and sucrose synthesis; photorespiration and C4
metabolism.
L
“
Practical (2-day)
1 x 4hr, 2 x 3hr, 1
x 1hr (PC to
follow P3), 3
occurances
Each student attends a 2 day practical (4x3 hr sessions) on the
kinetics of the enzyme alkaline phosphate. Development of a
spectroscopic assay; systematic investigation of how rates depend
on enzyme and substrate concentration; determination of kinetic
parameters Km and Vmax; studies of enzyme inhibition. This
practical involves both experimental design, and some data
handling.
Moir
Where tbc
Spring, when
tbc
Workshop 2
2 hours
Solving problems related to material taught in Spring term (lipids,
carbohydrates, metabolism, energy, photosynthesis).
Baumann, Maathuis,
Ungar
Where tbc
Summer term,
timing tbc
Ungar
Event
Duration (Hrs)
Topic
Staff
ASSESSMENT:
Summative: Closed examination (1.5 hrs) in January assessment period (week 1, spring term), weighted 40% of module mark
Closed examination (1.5 hrs) in summer assessment period (weeks 5-7 summer term), weighted 40% of module mark
Open assessment, spring term, weighted 20% of module mark
Re-assessment: Closed examination paper, August resit week
DEMONSTRATING REQUIREMENTS:
Autumn: 4 demonstrators
Spring: A total of 4-6 demonstrators needed for all of the practicals, two demonstrators being on duty at any time.
MAXIMUM NUMBERS: To capacity of lecture theatre/labs
STUDENT WORKLOAD: students’ workload totalling 100 hours per 10 credit module
Lectures: 32 hrs
Workshops: 4 hrs
Supported learning sessions (see workshops)
Practicals: 15 hrs
Tutorials
Total Contact hours: 51 hrs
Assessments (formative and summative): 2x 1.5 hrs
Private study: 146 hrs
Room type
Timing