BS31013 Biomembranes Handbook 2015-2016_docx

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SCHOOL OF LIFE SCIENCES

Life and Biomedical SciencesEducation

Module Handbook

BS31013 Biomembranes 2015/16

Module Manager: Prof. John A. Peters [email protected]

Teaching Support: [email protected]

This handbook belongs to: _____________________________

Email: ______________________________________________



BS31013 Biomembranes Module Handbook 2015/16

TABLE OF CONTENTSTable of Contents ............................................................................................. 1

Module teaching staff ....................................................................................... 1

Aims .......................................................................................................... 1

Intended learning outcomes (ILOs) ........................................................... 1

Learning resources & coursework.................................................................... 2

Workshops ................................................................................................ 2

Essay ........................................................................................................ 2

Lecture notes ............................................................................................ 2

Intended learning outcomes (ILOs) ........................................................... 2

Personal private study .............................................................................. 2

Compulsory classes and assessed elements .................................................. 3

Consequences of poor attendance or failure to submit coursework ......... 3

Penalties for late submission of course work ............................................ 3

Module assessment scheme ........................................................................... 3

Criteria for passing this module ................................................................ 4

Format of the degree examination ............................................................ 4

Recommended reading .................................................................................... 4

Core texts ................................................................................................. 4

Additional Reading .................................................................................... 4

Schedules for workshops etc* .......................................................................... 6

Membrane Transport - Workshop 1 .............................................................. 7




1

MODULE TEACHING STAFF

Module manager:Prof. John A. Peters [email protected]

Other teaching staff:Dr. Sheriar Hormuzdi [email protected] Prof. Hari Hundal [email protected] Prof. Jerry Lambert [email protected]

Teaching Support: [email protected]

Aims To provide the student with an understanding of the regulation of

normal membrane function and the physiological principles underlyingthis

To show how our current understanding of membrane function hasbeen arrived at, using examples from the current literature

To provide an understanding of some basic cellular and molecularphysiological and pharmacological techniques and their application toinvestigate membrane function

To enable the acquisition of skills, attitudes and techniques useful inthe pursuit of modern biology

Intended learning outcomes (ILOs)

After successful completion of this module students should be able todemonstrate the following items of knowledge and understanding.

Knowledge & understanding

Description of the structure and function of cell membranes

Explain characteristics such as: specificity of membrane transportsystems; generation of electrochemical gradients and their utilization;electrical events e.g. action and synaptic potentials

Identify processes that allow, or regulate, the movement of substancesacross cell membranes and between cells

Discriminate between ion channel processes and those ofsymport/antiport, active transport, passive diffusion and diffusion

Understand how ion distributions are achieved across membranes andtheir implications for the resting membrane potential

Describe the origin and the physiological impact of the ‘cableproperties’ of excitable cells

Give the evidence that provided current models for excitablemembrane function

Describe the modulation of neurotransmitter release and action




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SkillsStudents will be expected to perform complex data analysis and problemsolve.

Other attributes

Students will develop self-reliance and reinforce their independent study skills.

LEARNING RESOURCES & COURSEWORK

Workshops

There is one workshop in this module. It is intended (amongst other things) tofacilitate your understanding of the relevant lecture material. The workshop isspecifically designed to ensure that you gain understanding through activeparticipation, so please consult the workshop schedule in advance of the

session and arrive fully prepared to participate.

Essay

You are required to write one essay in this in this module. The essay titles willbe published with detailed instructions for its completion as an announcementon MY DUNDEE in week 1. The subject of the essay will be related to thelecture content. A Powerpoint file giving a ‘Guide to Good Essay Writing’ willbe posted in the Study Materials content area of the module to assist you. Theessay will account for 15% of the module assessment.

Lecture notes

The lectures for this module are available in outline as PowerPoint files,accessible via the Lectures content area of this module. You may find ithelpful to download and print these files (3 slides to a page) in advance ofattending the lecture so that you can make additional notes on the printout.This is a most effective way to ensure that you understand and retain thelecture material. DO NOT rely on these files as your sole source ofinformation!

Intended learning outcomes (ILOs)

ILOs for the lectures are included in the outline Powerpoint files (see above)which can be found in the Lectures content area of the module on MYDUNDEE. ILOs for practical classes and other elements of the courseworkare included in the schedules. You should make use of them to identify thekey elements that you are expected to understand and the skills that you areexpected to acquire.

Personal private study

BS31013 is a 15 credit module which corresponds to 150 hours of studenteffort. Since there are ~30 hours of contact time (lectures, workshops, and

examinations), this leaves you with roughly 120 hours for preparation,completion of formative and summative assessments and personal private




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study (which should include study of the relevant sections of your textbooksand any other recommended reading).

COMPULSORY CLASSES AND ASSESSED ELEMENTSPlease note that, for this module, attendance at all scheduled classes andsubmission of all coursework exercises listed in the module assessmentscheme is COMPULSORY.

These correspond to:

1. THE WORKSHOP

2. ALL COURSEWORK SUBMISSIONS(Sequence numbers 002 to 003 in the table below)

All coursework must be handed in to the Level 3 black box in theCarnelley Building on City Campus, or submitted via ‘Turnitin’ asinstructed.

Consequences of poor attendance or failure to submit coursework

More than one unexplained or uncertified absence from any of the compulsoryclasses and/or non-submission of coursework will result in you beingsummoned for interview to identify the underlying reasons. Thereafter, anyfurther unexplained or uncertified absences may result in your Duly Performed(DP) status being withdrawn. This would mean that you would not be allowedto sit the Degree examination in the December diet OR the resit diet in Augustand therefore could not pass the module.

Penalties for late submission of course work

Any unauthorised late submission may incur penalties of one numerical pointper day for up to a maximum of 5 days following the published deadline. Notethat Saturday and Sunday will each count as one of these 5 days if they fall inthe 5 days following the deadline. For example, if your assignment wassubmitted 5 days late and was rated as an A5 grade, then this would bedowngraded to C2 for late submission.

All submissions which are more than a working week late will be marked forfeedback purposes but you will be awarded a BF grade towards the overallmodule mark for the associated coursework. Non-submission will be gradedas AB. Requests for extensions to deadlines must be made to the modulemanager.

MODULE ASSESSMENT SCHEME

Assessed Element No. %

WeightDeadline




4

Degree examination 001 80December exam diettimetable

Workshop 002 5 12 noon - Fri 16th Oct

Essay 003 15 12 noon - Fri 23th Oct

Criteria for passing th is moduleIn order to pass this module, you must fulfil the following criteria:

1. You must achieve a minimum of a D3 grade* for the overall modulewhich is calculated as a weighted average of all the assessed elementsin the table above.

*Note that progression to the next level in your chosen degree programmemay require you to achieve a higher grade average than D3 at first sittingacross your core modules. Please see the official degree regulations for youryear of entry in the Information for Life Sciences student’s module on MyDundee.

Further explanation of the criteria for passing Life Sciences modules and ofthe regulations governing resit or reassessment in the event of failure can befound in the Life Sciences Study Guide.

Format of the degree examination

The degree exam at the end of the semester takes the form of a 2 hourwritten exam using computer submission of answers. The exam will containtwo sections; one section will contain four short answer questions of which

you must answer two, and the second will consist of thirty MCQs, all of whichmust be attempted. MCQs will typically be in the format of identifying one validoption from a list of five. A period of one hour will be allocated to each of theabove sections.

RECOMMENDED READINGCore texts are considered to be absolutely essential and can be purchasedonline, or at the campus bookshop, during Welcome week. You may also beable to obtain used copies from previous students. These may be advertised

on noticeboards in the Student’s Union, or elsewhere on campus.

Core texts

Medical Physiology (Updated 2nd. international ed.) Boron WF, Boulpaep EL.(2012). Elsevier Saunders ISBN-978-0-8089-2449-4.

Addit ional Reading

From Neuron to Brain (5th. ed.) Nicholls JG, Martin RA, Fuchs PA, Brown DA,Diamond ME, Weisblat DA. (2012). Sinauer ISBN 978-0-87893-609-0.




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Neuroscience: Exploring the Brain (4th. ed.) Bear MF, Connors BW, ParadisoMA. (2016). Wolters Kluwer. ISBN 978-1-4511-0954-2.



BS31013 Module Handbook 2015/16

6

SCHEDULES FOR WORKSHOPS ETC*The following section includes the schedules of the workshops, tutorials andstudy exercises associated with this module.

Please ensure that you read these schedules and complete any pre-classexercises BEFORE attending the class and/or completing any associatedworksheet. You should bring the schedule to the class along with anycompleted worksheets (if required). Spare copies of the schedule WILL NOTbe provided in the class.



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Membrane Transport - Workshop 1

This workshop will take the form of a manual exercise that

demonstrates, in a simple manner, several key concepts in membranetransport.

A ‘Hands on’ Approach to Biomembrane Transport

Introduction

In this workshop, we will investigate the basic principles of biomembrane transport

using a simple manual model system. In this system, trays represent the aqueous

compartments (ECF and ICF) on the two sides of the membrane and the coloured

counters represent solute molecules that a “transporter” (a member of your group)

transfers by hand‐to‐hand movements across the (virtual) membrane from one

compartment (tray A) to the other (tray B).

The team member designated as the “transporter” moves coloured counters from one

tray to another, with eyes closed, over a timed period of 10 seconds. This experiment

can be repeated with different numbers (concentration) and colour (different solute)

combinations of counters, allowing investigation of factors such as saturation and

competition (between solutes).

The following

diagram

shows

a simple

mechanism

of

uniport:

‐can

you

identify

the

steps in the diagram within your system models?

Consider the following questions:

1. What factors limit the transport rate? What happens when you add more

solute (S) to a system working at full capacity?

2. What is the rate constant for an individual transporter (solute moved per

second)?



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3. How might you model in increase in the maximum rate of transport (Vmax)?

4. Would a transport event occur every time a solute was “bound” from the

starting tray? (i.e. is the transporter 100% efficient?).

Theoretical background

In the simple situation of uniport described above, the rate (V ) at which a solute (S) is

transported across the membrane is a function of solute concentration in the ECF ([S ]).

The process overall follows first order kinetics and can be described in terms of

Michaelis‐Menton kinetics as written below:

Where V is rate of transport, V max is maximal rate of transport at saturating solute

concentration, [S ] is solute concentration and K m is the Michaelis constant at which

the rate of transport is half maximal. Expressed as above, it is easy to see that V is half

maximal when [S ] equals K m . The equation may be alternatively stated as:

Graphically,

a

plot

of

V

(ordinate,

y‐

axis)

versus

S

(abscissa,

x‐

axis),

both

on

linear

axes,

yields a semi‐rectangular hyperbola, as illustrated below (labelled facilitated diffusion;

aka facilitative transport):



9

Note that in contrast to simple diffusion in which V is a simply directly proportional to

S , facilitated is characterised by saturation at concentrations of S that greatly exceed

K m . Saturation occurs when all uniporters (in this case) within the population are

occupied by solute. The translocation step then becomes rate limiting.

Using appropriate equation fitting software, it is possible to calculate K m and V max

from the plot as shown above. An alternative is to perform a simple transformation

that results in a linear relationship from which these parameters may be estimated.

One of several is the Eadie‐Hoftsee Plot which in which the velocity of solute transport

(V ) is plotted against V divided by [S ] (i.e. (V /[S ]) as shown below:

Note, this results from a simple rearrangement of the equations written above,

namely:

which has the form of:

The workshop

Part 1

1. Please divide into six groups (three to four students per group).

2. Within each group allocate a ‘transporter’, a ‘timer’ and a ‘feeder’. The

‘transporter’ translocates solute molecules from plate A to plate B ‐ rapidly

(but at as steady a rate as possible) within a set time of 10 seconds without



10

visual guidance. Pass the solute from left to right hand (or vice versa) during

this exercise and do not have more than one solute in your hands at the same

time. The ‘timer’ starts and finishes the translocation period. The ‘feeder’

replenishes the plate from which solute molecules are being removed on a one

per one

basis

(why

do

you

think

this

is

necessary

from

examination

of

the

equations above?). Both ‘feeder’ and ‘transporter should wear gloves if you

wish to consume the solute in a hygienic manner at the end of the workshop!

3. The feeder allocates solute molecules to plate A in a randomly distributed

fashion and replenishes as necessary. At this stage the colour (i.e. chemical

structure) of the solute can be one of any of those provided. Use

concentrations (S ) of 1, 2, 5, 10, 20 and 40 solute molecules for each period of

transport.

4. For each concentration, record the number of solute molecules transported

for each

time

period.

5. All groups attending on one day should collate their data in an Excel sheet

(during the workshop) to determine the mean rate of transport (in units of

solutes transported per second) for each concentration of solute.

6. Following the workshop, construct plots of transport rate (V ) versus substrate

concentration (S ) using graphics packages such as found within Excel. This

should be performed using the mean data obtained by all groups on one day

(i.e. the Monday, Tuesday etc . sheets as posted in the Excel file and the

Summary data sheet for all groups which is also posted.

Part

2

1. Please remain within groups.

2. Chose one colour that represents solute X and one that represents solute Y.

Solute X and Y compete for transport via a common transporter (i.e. their

binding is mutually exclusive).

3. Place twenty molecules of solute X and an equal number of solute Y on plate

A.

4. Perform a period of transport of 20 seconds, replenishing as required with the

appropriate solute.

5. All groups should collate their data in an Excel sheet (during the workshop) to

determine the mean rate of transport (in units of solutes per second) of solute

X and solute Y.

6. Following the workshop, comment upon the effect of solute X upon the rate

of transport of solute Y, or vice versa.

Report

As hard copy, submit a report by the specified date (i.e. Friday of week 5, 17th.

October) that

includes

all

of

the

following:



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1. Plots of the relationship between solute concentration and transport rate as

specified in part 1, including your approximate estimate of K m and V max

obtained from examination of your plots. It is not required that you include

error bars. Please include tables of the data from which the plots are derived.

(40 %)

2. An Eadie‐Hoftsee plot (see above) to determine K m and V max with improved

accuracy using the idealised data provided. (20%). State the values of K m and

V max so obtained.

3. In no more than two sentences, a description of how you would anticipate

solute X to influence the K m for solute Y given that they are present at a

submaximal concentration that is the same for both and that they have equal

affinity for the transporter. (10%)

4. A calculation of the K m for a substrate given the following information:

[S ] = 20

µM

V = 2500 s‐1

V max = 10000 s‐1

(15%)

5. A calculation of the V max for a substrate given the following information:

[S ] = 50 µM

V = 5000

s‐1

K m = 100 µM

(15%)

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